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EXHIBIT 31.1 CERTIFICATION OF CHIEF EXECUTIVE OFFICER
PURSUANT TO SECTION 302
OF THE SARBANES-OXLEY ACT OF 2002 I, David Mitchell, President and Chief Executive Officer of webMethods, Inc., have executed this
certification in connection with the filing with the Securities and Exchange Commission of the
registrants annual report on Form 10-K for the fiscal year ended March 31, 2005. I certify that:  1.
    I have reviewed this annual report on Form 10-K of webMethods, Inc.;2.
    Based on my knowledge, this annual report does not contain any untrue statement of a
material fact or omit to state a material fact necessary to make the statements made, in
light of the circumstances under which such statements were made, not misleading with
respect to the period covered by this annual report;3.
    Based on my knowledge, the financial statements, and other financial information included
in this annual report fairly present in all material respects the financial condition,
results of operations and cash flows of the registrant as of, and for, the periods presented
in this annual report;4.
    The registrants other certifying officers and I are responsible for establishing and
maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e)
and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act
Rules 13a-15(f) and 15d-15(f)) for the registrant and have:  a)
    Designed such disclosure controls and procedures, or caused such
disclosure controls and procedures to be designed under our
supervision, to ensure that material information relating to the
registrant, including its consolidated subsidiaries, is made known to
us by others within those entities, particularly during the period in
which this report is being prepared;b)
    Designed such internal control over financial reporting, or caused
such internal control over financial reporting to be designed
under our supervision, to provide reasonable assurance regarding
the reliability of financial reporting and the preparation of
financial statements for external purposes in accordance with
generally accepted accounting principles;c)
    Evaluated the effectiveness of the registrants disclosure
controls and procedures and presented in this report our
conclusions about the effectiveness of the disclosure controls and
procedures, as of the end of the period covered by this report
based on such evaluation; andd)
    Disclosed in this report any change in the registrants internal
control over financial reporting that occurred during the
registrants most recent fiscal quarter (the registrants fourth
fiscal quarter in the case of an annual report) that has
materially affected, or is reasonably likely to materially affect,
the registrants internal control over financial reporting; and  5.
    The registrants other certifying officers and I have disclosed, based on our most recent
evaluation of internal control over financial reporting, to the registrants auditors and
the audit committee of the registrants board of directors (or persons fulfilling the
equivalent function):  (a)
    All significant deficiencies and material weaknesses in the design or operation of
internal control over financial reporting which are reasonably likely to adversely affect
the registrants ability to record, process, summarize and report financial information;
and(b)
    Any fraud, whether or not material, that involves management or other employees who
have a significant role in the registrants internal control over financial reporting. Date: June 13, 2005 /s/ DAVID MITCHELL
Name: David Mitchell
Title: President and Chief Executive Officer