<Page>

                                                                     Exhibit 4.2

                             ADVANCED BIOENERGY, LLC

                             SUBSCRIPTION AGREEMENT

                   Limited Liability Company Membership Units

                                 $10.00 PER UNIT

                   MINIMUM INVESTMENT OF 2,500 UNITS ($25,000)
                     100 UNIT INCREMENTS THEREAFTER ($1,000)

The undersigned subscriber, desiring to become a member of Advanced BioEnergy,
LLC ("Advanced BioEnergy"), a Delaware limited liability company, with its
principal place of business at 910 9th Street, Fairmont, Nebraska 68354, hereby
subscribes for the purchase of the membership interests of Advanced BioEnergy,
and agrees to pay the related purchase price, identified below.

A.   SUBSCRIBER INFORMATION. Please print your individual or entity name and
address. Joint subscribers should provide their respective names. Your name and
address will be recorded exactly as printed below.

   1.    Subscriber's Printed Name   ___________________________________________
   2.    Title, if applicable:       ___________________________________________
   3.    Subscriber's Address:
              Street                 ___________________________________________
              City, State, Zip Code  ___________________________________________
   4.    Email Address:              ___________________________________________

B.   NUMBER OF UNITS PURCHASED. You must purchase at least 2500 units. We
presently have 634,650 units outstanding. The maximum number of units to be sold
is 6,732,500.

          _____________

C.   PURCHASE PRICE. Indicate the dollar amount of your investment (minimum
investment is $25,000).

<Table>
<Caption>
      1. Total Purchase Price         =            2. 1st Installment          +           3. 2nd Installment
         --------------------                         ---------------                         ---------------
<S>                                         <C>                                       <C>
($10.00 Per Unit multiplied by the          (10% of the Total Purchase Price)         (90% of the Total Purchase
number in box B above.)                                                               Price)

____________________________________    =   _________________________________    +    _____________________________
</Table>

D.   GENERAL INSTRUCTIONS FOR SUBSCRIBERS:

You should read the Prospectus dated [DATE OF EFFECTIVENESS] (the "Prospectus")
in its entirety including exhibits for a complete explanation of an investment
in Advanced BioEnergy, LLC. To subscribe, you must:

INSTRUCTIONS IF YOU ARE SUBSCRIBING PRIOR TO THE COMPANY'S RELEASE OF FUNDS FROM
ESCROW: If you are subscribing prior to the Company's release of funds from
escrow, you must follow Steps 1 through 5 below:

     1.   Complete all information required in this Subscription Agreement, and
date and sign the Subscription Agreement on page 6 and the Member Signature Page
to our Amended and Restated Operating Agreement attached to this Subscription
Agreement as Exhibit A.

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     2.   Immediately provide your personal (or business) check for the first
installment of ten percent (10%) of your investment amount made payable to
Geneva State Bank, escrow agent for Advanced BioEnergy LLC. You will determine
this amount in box C.2 on page 1 of this Subscription Agreement.

     3.   Execute the Promissory Note and Security Agreement on page 7 of this
Subscription Agreement evidencing your commitment to pay the remaining ninety
percent (90%) due for the Units that is attached to this Subscription Agreement
and grant Advanced BioEnergy, LLC a security interest in your Units.

     4.   Deliver each of the original executed documents referenced in Items 1
and 3 of these Instructions, together with your personal or business check
described in Item 2 of these Instructions to either of the following:

          Advanced BioEnergy, LLC            Geneva State Bank
          137 N. 8th Street                   Attn:  Aaron Schardt
          Geneva, Nebraska 68361             896 "G" Street
                                             Geneva, Nebraska  68361

     5.   Upon written notice from Advanced BioEnergy, LLC stating that its
sales of Units have exceeded the Minimum Offering amount of $33,662,500, you
must, within twenty (20) days secure an additional personal (or business) check
for the second installment of ninety percent (90%) of your investment amount
made payable to Geneva State Bank, escrow agent for Advanced BioEnergy, LLC in
satisfaction of the Promissory Note and Security Agreement. You will determine
this amount in box C.3 on page 1 of this Subscription Agreement. You must
deliver this check to the same address set forth above in Instruction 4 within
twenty (20) days of the date of Advanced BioEnergy's written notice. If you fail
to pay the second installment pursuant to the Promissory Note and Security
Agreement, Advanced BioEnergy shall be entitled to retain your first installment
and to seek other damages, as provided in the Promissory Note and Security
Agreement.

Your funds will be placed in Advanced BioEnergy's escrow account at Geneva State
Bank. The funds will be released to Advanced BioEnergy or returned to you in
accordance with the escrow arrangements described in the Prospectus. Advanced
BioEnergy may, in its sole discretion, reject or accept any part or all of your
subscription. If Advanced BioEnergy rejects your subscription, your Subscription
Agreement and investment will be promptly returned to you, plus nominal
interest, minus escrow fees. Advanced BioEnergy may not consider the acceptance
or rejection of your subscription until a future date near the end of this
offering.

INSTRUCTIONS IF YOU ARE SUBSCRIBING AFTER THE COMPANY'S RELEASE OF FUNDS FROM
ESCROW: If you are subscribing after the Company's release of funds from escrow,
you must follow Steps 1 through 3 below:

     1.   Complete all information required in this Subscription Agreement, and
date and sign the Subscription Agreement on page 6 and the Member Signature Page
to our Amended and Restated Operating Agreement attached to this Subscription
Agreement as Exhibit A.

     2.   Immediately provide your personal (or business) check for the entire
amount of your investment (as determined in Box C.1 on page 1) made payable to
"ADVANCED BIOENERGY, LLC."

     3.   Deliver the original executed documents referenced in Item 1 of these
Instructions, together with your personal or business check described in Item 2
of these Instructions to the following:

                      Advanced BioEnergy, LLC
                      137 N. 8th Street
                      Geneva, Nebraska 68361

     If you are subscribing after we have released funds from escrow and we
accept your investment, your funds will be immediately at-risk as described in
the Prospectus. Advanced BioEnergy may, in its sole discretion, reject or accept
any part or all of your subscription. If Advanced BioEnergy rejects your
subscription, your Subscription Agreement and investment will be returned to you
promptly, plus nominal interest, minus escrow fees. Advanced BioEnergy may not
consider the acceptance or rejection of your subscription until a future date
near the end of this offering.

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YOU MAY DIRECT YOUR QUESTIONS TO ONE OF OUR DIRECTORS LISTED BELOW OR TO
ADVANCED BIOENERGY AT 402-268-3101.

<Table>
<Caption>
                       Director             Phone Number
                       --------             ------------
                  <S>                       <C>
                  John T. Porter            402-432-5247

                  Troy Otte                 402-362-3885

                  John E. Lovegrove         402-366-4484

                  Robert E. Bettger         402-268-3101

                  Larry L. Cerny            402-759-1165

                  Richard W. Hughes         402-759-4615

                  Keith E. Spohn            402-947-8061
</Table>

E.   ADDITIONAL SUBSCRIBER INFORMATION. The subscriber, named above, certifies
the following under penalties of perjury:

     1.   FORM OF OWNERSHIP. Check the appropriate box (one only) to indicate
          form of ownership. If the subscriber is a Custodian, Corporation,
          Partnership or Trust, please provide the additional information
          requested.

          / /  Individual
          / /  Joint Tenants with Right of Survivorship (Both signatures must
               appear on Page 6.)
          / /  Corporation, Limited Liability Company or Partnership (Corporate
               Resolutions, Operating Agreement or Partnership Agreement must be
               enclosed.)
          / /  Trust
                  Trustee's Name:__________________________________________
                  Trust Date:______________________________________________
          / /  Other: Provide detailed information in the space immediately
               below.
               ____________________________________________________________
               ____________________________________________________________
               ____________________________________________________________

     2.   SUBSCRIBER'S TAXPAYER INFORMATION. Check the appropriate box if you
          are a non-resident alien, a U.S. Citizen residing outside the United
          States or subject to backup withholding. Trusts should provide their
          taxpayer identification number. Custodians should provide the minor's
          Social Security Number. All individual subscribers should provide
          their Social Security Number. Other entities should provide their
          taxpayer identification number.

          / /  Check box if you are a non-resident alien
          / /  Check box if you are a U.S. citizen residing outside of the
               United States
          / /  Check this box if you are subject to backup withholding

          Subscriber's Social Security No.         ________________________
          Joint Subscriber's Social Security No    ________________________
          Taxpayer Identification No.              ________________________

     3.   MEMBER REPORT ADDRESS. If you would like duplicate copies of member
          reports sent to an address that is different than the address
          identified in section A, please complete this section.

          Address:     _______________________________________
                       _______________________________________

     4.   STATE OF RESIDENCE.

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          State of Principal Residence:                ____________________
          State where driver's license is issued:      ____________________
          State where resident income taxes are filed: ____________________

          State(s) in which you have maintained your principal residence during
          the past three years:

<Table>
          <S>                    <C>                    <C>
          a                      b.                     c.
</Table>

     5.   SUITABILITY STANDARDS. You cannot invest in Advanced BioEnergy unless
          you meet one, or more, of the following suitability tests (a, b, or c)
          set forth below. Please review the suitability tests and check the
          box(es) next to the following suitability test that you meet. For
          husbands and wives purchasing jointly, the tests below will be applied
          on a joint basis.

          a.      I (We) are "Producers" as defined hereunder. For purposes of
                  this Subscription Agreement, a "Producer" is defined as a
                  person who is ONE of the following:

                  / /  A natural person or a fiduciary of a natural person who
                       regularly participates in physical labor, operations or
                       management in a farming operation and files Schedule F as
                       part of the person's annual income tax return.

                  / /  A person who owns at least 150 acres of agricultural land
                       and receives as rent a share of the crops or the animals
                       raised on the land.

                  / /  A duly authorized officer of a family farm corporation,
                       member or manager of a family farm limited liability
                       company, general manager of a family farm limited
                       partnership or trustee of a family trust actively engaged
                       in farming.

                  / /  A general partnership in which all the partners are
                       natural persons actively engaged in farming;

          b. / /  I (We) have annual income from whatever source of at least
                  $45,000 AND a net worth of at least $45,000, exclusive of
                  home, furnishings and automobiles; or

          c. / /  I (We) have a net worth of at least $100,000, exclusive of
                  home, furnishings and automobiles.

     6.   SUBSCRIBER'S REPRESENTATIONS AND WARRANTIES. You must read and certify
          your representations and warranties and sign and date this
          Subscription Agreement.

          By signing below the subscriber represents and warrants to Advanced
          BioEnergy that he, she or it:

          a.   has received a copy of Advanced BioEnergy's Prospectus dated
               __________ and the exhibits thereto;
          b.   has been informed that the Units of Advanced BioEnergy are
               offered and sold in reliance upon a federal securities
               registration; Nebraska, South Dakota, Iowa, Texas, Wisconsin,
               Kansas and Florida securities registrations; and exemptions
               from securities registrations in various other states, and
               understands that the Units to be issued pursuant to this
               subscription agreement can only be sold to a person meeting
               requirements of suitability;
          c.   has been informed that the securities purchased pursuant to this
               Subscription Agreement have not been registered under the
               securities laws of any state other than the States of Nebraska,
               South Dakota, Iowa, Texas, Wisconsin, Kansas and Florida,
               and that Advanced BioEnergy is relying in part upon the
               representations of the undersigned Subscriber contained herein;
          d.   has been informed that the securities subscribed for have not
               been approved or disapproved by the Nebraska, South Dakota,
               Iowa, Texas, Wisconsin, Kansas and Florida Securities Departments
               or any other regulatory authority, nor has any regulatory
               authority passed upon the accuracy or adequacy of the Prospectus;
          e.   intends to acquire the Units for his/her/its own account without
               a view to public distribution or resale and that he/she/it has no
               contract, undertaking, agreement or arrangement to sell or
               otherwise transfer or dispose of any Units or any portion thereof
               to any other person;

                                        4
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          f.   understands that there is no present market for Advanced
               BioEnergy's membership units, that the membership units will not
               trade on an exchange or automatic quotation system, that no such
               market is expected to develop in the future and that there are
               significant restrictions on the transferability of the membership
               units;
          g.   has been encouraged to seek the advice of his legal counsel
               and accountants or other financial advisers with respect to the
               tax and other considerations relating to the purchase of units;
          h.   has received a copy of the Advanced BioEnergy Operating
               Agreement, dated February 18, 2005, and understands that upon
               closing the escrow by Advanced BioEnergy, the subscriber and the
               membership units will be bound by the provisions of the Operating
               Agreement which contains, among other things, provisions that
               restrict the transfer of membership units;
          i.   understands that the Units are subject to substantial
               restrictions on transfer under state securities laws along with
               restrictions in the Advanced BioEnergy Operating Agreement and
               agrees that if the membership units or any part thereof are sold
               or distributed in the future, the subscriber shall sell or
               distribute them pursuant to the terms of the Operating Agreement,
               and the requirements of the Securities Act of 1933, as amended,
               and applicable state securities laws;
          j.   meets the suitability test marked in Item 5 above and is capable
               of bearing the economic risk of this investment, including the
               possible total loss of the investment;
          k.   understands that Advanced BioEnergy will place a restrictive
               legend on any certificate representing any unit containing
               substantially the following language as the same may be amended
               by the Directors of Advanced BioEnergy in their sole discretion:

                  THE TRANSFERABILITY OF THE UNITS REPRESENTED BY THIS
                  CERTIFICATE IS RESTRICTED. SUCH UNITS MAY NOT BE SOLD,
                  ASSIGNED, OR TRANSFERRED, NOR WILL ANY ASSIGNEE, VENDEE,
                  TRANSFEREE, OR ENDORSEE THEREOF BE RECOGNIZED AS HAVING
                  ACQUIRED ANY SUCH UNITS FOR ANY PURPOSES, UNLESS AND TO THE
                  EXTENT SUCH SALE, TRANSFER, HYPOTHECATION, OR ASSIGNMENT IS
                  PERMITTED BY, AND IS COMPLETED IN STRICT ACCORDANCE WITH,
                  APPLICABLE STATE AND FEDERAL LAW AND THE TERMS AND CONDITIONS
                  SET FORTH IN THE AMENDED AND RESTATED OPERATING AGREEMENT AS
                  AGREED TO BY EACH MEMBER.

                  THE SECURITIES REPRESENTED BY THIS CERTIFICATE MAY NOT BE
                  SOLD, OFFERED FOR SALE, OR TRANSFERRED IN THE ABSENCE OF
                  EITHER AN EFFECTIVE REGISTRATION UNDER THE SECURITIES ACT OF
                  1933, AS AMENDED, AND UNDER APPLICABLE STATE SECURITIES LAWS,
                  OR AN OPINION OF COUNSEL SATISFACTORY TO THE COMPANY THAT SUCH
                  TRANSACTION IS EXEMPT FROM REGISTRATION UNDER THE SECURITIES
                  ACT OF 1933, AS AMENDED, AND UNDER APPLICABLE STATE SECURITIES
                  LAWS.

          l.   understands that, to enforce the above legend, Advanced BioEnergy
               may place a stop transfer order with its registrar and stock
               transfer agent (if any) covering all certificates representing
               any of the membership units;
          m.   has examined the information presented in the prospectus and
               exhibits and is competent to evaluate and establish that the
               investment is consistent with the subscriber's risk tolerance
               and investment goals such that the subscriber can bear the
               economic risk of the purchase of Units including the total loss
               of the undersigned's investment;
          n.   may not transfer or assign this subscription agreement, or any of
               the subscriber's interest herein;
          o.   has written his, her, or its correct taxpayer identification
               number under Item E.2 on this subscription agreement;
          p.   is not subject to back up withholding either because he, she or
               it has not been notified by the Internal Revenue Service ("IRS")
               that he, she or it is subject to backup withholding as a result
               of a failure to report all interest or dividends, or the IRS has
               notified him, her or it that he is no longer subject to backup
               withholding (Note this clause (p) should be crossed out if the
               backup withholding box in Item 2 is checked);

                                        5
<Page>

          q.   understands that execution of the attached Promissory Note and
               Security Agreement will allow Advanced BioEnergy or its assigns
               to pursue the obligor for payment of the amount due thereon by
               any legal means, including, but not limited to, acquisition of a
               judgment against the obligor in the event that the subscriber
               defaults on that Promissory Note and Security Agreement; and
          r.   Acknowledges that Advanced BioEnergy may retain possession of
               certificates representing subscriber's Units to perfect its
               security interest in those Units.

SIGNATURE OF SUBSCRIBER/JOINT SUBSCRIBER:

DATE:
          -----------------------------------

<Table>
<Caption>
INDIVIDUALS:                                                  ENTITIES:
     <S>                                                      <C>


-------------------------------------------------------       ---------------------------------------
     Name of Individual Subscriber (Please Print)             Name of Entity (Please Print)


-------------------------------------------------------       ---------------------------------------
     Signature of Individual                                  Print Name and Title of Officer


-------------------------------------------------------       ---------------------------------------
     Name of Joint Individual Subscriber (Please Print)       Signature of Officer


-------------------------------------------------------
     Signature of Joint Individual Subscriber
</Table>

ACCEPTANCE OF SUBSCRIPTION BY ADVANCED BIOENERGY, LLC:


Advanced BioEnergy, LLC hereby accepts the subscription for the above Units.

Dated this_________day of________________________, 200____.


ADVANCED BIOENERGY, LLC


By:
    ----------------------------------------------------

Its:
    ----------------------------------------------------

                                        6
<Page>

                     PROMISSORY NOTE AND SECURITY AGREEMENT

Date of Subscription Agreement: ___________________________________, 200__.
                                          $10.00 PER UNIT

        MINIMUM INVESTMENT OF 2,500 UNITS ($25,000), 100 UNIT INCREMENTS
                               THEREAFTER ($1,000)

_______________ Number of Units subscribed

_______________ Total Purchase Price ($10.00 per Unit multiplied by number of
Units subscribed)

___(________)__ Less Initial Payment (10% of Principal Amount)

_______________ Principal Balance

FOR VALUE RECEIVED, the undersigned hereby promises to pay to the order of
Advanced BioEnergy, LLC, a Delaware limited liability company ("Advanced
BioEnergy"), at its principal office located 910 9th Street, Fairmont, Nebraska
68354, or at such other place as required by Advanced BioEnergy, the Principal
Balance set forth above in one lump sum to be paid without interest within 20
days following the call of the Advanced BioEnergy Board of Directors, as
described in the Subscription Agreement. In the event the undersigned fails to
timely make any payment owed, the entire balance of any amounts due under this
full recourse Promissory Note and Security Agreement shall be immediately due
and payable in full with interest at the rate of 12% per annum from the due date
and any amounts previously paid in relation to the obligation evidenced by this
Promissory Note and Security Agreement may be forfeited at the discretion of
Advanced BioEnergy.

The undersigned agrees to pay to Advanced BioEnergy on demand, all costs and
expenses incurred to collect any indebtedness evidenced by this Promissory Note
and Security Agreement, including, without limitation, reasonable attorneys'
fees. This Promissory Note and Security Agreement may not be modified orally and
shall in all respects be governed by, construed, and enforced in accordance with
the laws of the State of Delaware.

The provisions of this Promissory Note and Security Agreement shall inure to the
benefit of Advanced BioEnergy and its successors and assigns, which expressly
reserves the right to pursue the undersigned for payment of the amount due
thereon by any legal means in the event that the undersigned defaults on
obligations provided in this Promissory Note and Security Agreement.

The undersigned waives presentment, demand for payment, notice of dishonor,
notice of protest, and all other notices or demands in connection with the
delivery, acceptance, performance or default of this Promissory Note and
Security Agreement.

The undersigned grants to Advanced BioEnergy, and its successors and assigns
("Secured Party"), a purchase money security interest in all of the
undersigned's Membership Units of Advanced BioEnergy now owned or hereafter
acquired. This security interest is granted as non-exclusive collateral to
secure payment and performance on the obligation owed Secured Party from the
undersigned evidenced by this Promissory Note and Security Agreement. The
undersigned further authorizes Secured Party to retain possession of
certificates representing such Membership Units and to take any other actions
necessary to perfect the security interest granted herein.

Dated:      , 200  .

<Table>
<Caption>
OBLIGOR/DEBTOR:                             JOINT OBLIGOR/DEBTOR:
<S>                                         <C>

-----------------------------------------   ------------------------------------
Printed or Typed Name of Joint Obligor      Printed or Typed Name of Obligor


By:                                         By:
    -------------------------------------       --------------------------------
    (Signature)                                 (Signature)


-----------------------------------------
Officer Title if Obligor is an Entity

-----------------------------------------

-----------------------------------------
</Table>

                                        7
<Page>

Address of Obligor

                                   EXHIBIT "A"

                              MEMBER SIGNATURE PAGE

                                 ADDENDA TO THE
              AMENDED AND RESTATED OPERATING AGREEMENT OF ADVANCED
                                 BIOENERGY, LLC

     The undersigned does hereby represent and warrant that the undersigned, as
a condition to becoming a Member in Advanced BioEnergy, LLC, has received a copy
of the Amended and Restated Operating Agreement dated May 19, 2005, and, if
applicable, all amendments and modifications thereto, and does hereby agree that
the undersigned, along with the other parties to the Amended and Restated
Operating Agreement, shall be subject to and comply with all terms and
conditions of said Amended and Restated Operating Agreement in all respects as
if the undersigned had executed said Amended and Restated Operating Agreement on
the original date thereof and that the undersigned is and shall be bound by all
of the provisions of said Amended and Restated Operating Agreement from and
after the date of execution hereof.

<Table>
<Caption>
INDIVIDUALS:                                    ENTITIES:
<S>                                                           <C>


--------------------------------------------------    ---------------------------------------
Name of Individual Member (Please Print)              Name of Entity (Please Print)


--------------------------------------------------    ---------------------------------------
Signature of Individual                               Print Name and Title of Officer


--------------------------------------------------    ---------------------------------------
Name of Joint Individual Member (Please Print)        Signature of Officer


--------------------------------------------------
Signature of Joint Individual Member
</Table>

AGREED AND ACCEPTED ON BEHALF OF THE
COMPANY AND ITS MEMBERS:

ADVANCED BIOENERGY, LLC


By:
    ----------------------------------------------


Its:
    ----------------------------------------------

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