On October 13, 2017, Hallo Hallo Entertainment announced registration and audition tour dates for the group's first generation. On November 10, 2017, Hallo Hallo Entertainment held the first audition for MNL48.
In early 2018, a segment was hosted on "It's Showtime" by Anne Curtis, Billy Crawford, Karylle and Jhong Hilario which determined the members of the group's first generation. It is a segment of search for the ultimate all-female Filipino idol group whose name is derived from its based city of Manila. It conducted nationwide auditions for women aged 15–20 years old to become sought-after idols you can meet. Thousands of women took part of the audition, but only 200 of them succeeded to start the 13-week challenge rounds for them to test their singing & dancing skills. From Top 200, the aspirants were reduced to Top 75 in order to face public voting until General Election using MNL48-Plus App which was developed by Hallohallo Entertainment Inc. in partnership with ABS-CBN and one of the world's top multimedia, entertainment and IT agencies, AKS. From Top 75, only 48 women will become the official members of this group. From Top 48, There will be a ranking system that follows AKB48's Senbatsu Sousenkyo concept. Top 33-48 will be hailed as Next Girls, Top 17-32 will be hailed as the Under Girls & Top 16 will be hailed as Senbatsu members. From Top 16, 7 women will secure the Kami 7 slots which they will become the frontliners of the performance to join concerts with AKB48 & all of its sister groups worldwide, they will also be given international endorsement deals & an exclusive training program in AKS. And from Kami 7, the winner (as the Center Girl) of the general election will be the face of MNL48 worldwide.
On April 22, the "Meet Your Oshimen" event was held, where three hundred lucky ticket-holding fans met and greeted their favourite MNL48 aspirants. The handshake event was held at the TriNoma at 5:00 PM on the 4th Floor Garden. Six days after the event, the first general election took place at Studio 4 and Center Road in ABS-CBN. Before the election on April 28, Kris (as a challenger), along with two other eligible contenders Aria and Eunice, announced their departure from the group and will resign from their candidacy for the upcoming election. A few days after the election, eight trainees Reiko, Reina, Nix, Ann, Celine, Arol, Kana, and Ikee also left the group. The newly recruited trainee Cole came in as a replacement member.
On June 3, MNL48's fan-meeting event was held at the Eton Centris Elements. The group performed the Tagalog versions of "Aitakatta", "Heavy Rotation", "Skirt Hirari", and "Sakura no Hanabiratachi" for the first time. On June 8, the members Trixie, Zen, Van, and Mae announced their departure from the group. To fill in the spots, the "kenkyuusei" members Rans, Nina, and Andi were promoted as members of Team MII. Trainee Coleen is then promoted to Team NIV. For the rankings, Ella and Ash entered the "Kami" 7, while Alyssa and Erica joined the Senbatsu. On July 9, Nina and Vern announced their departure from MNL48, with Cassey filling Nina's position in Team MII.
On August 17, the group premiered the music video of their debut single "Aittakata – Gustong Makita". While their debut extended play "Aitakatta" was released on September 14, the single was released on September 28. On October 5, MNL48 were announced as one of the participants for "Himig Handog 2018". The group interpreted the song "Dalawang Pag-ibig Niya" alongside "Your Face Sounds Familiar Kids" alumni Krystal Brimner and Sheena Belarmino. On October 26, MNL48 premiered their second music video "Talulot ng Sakura". On November 7, 18 days before the official release of the second single, trainee Sheccaniah Faith Baler planned to resign from the group since she completed her duties in the group's debut. On November 25, the group premiered the music video of their second single "Pag-ibig Fortune Cookie" the same day they performed the said single on another "Handshake Event" held on Movie Stars Cafe. On December 12, 2018, trainee Edralyn Tocop left, leaving nine trainees remaining.
On December 11, AKS announced that the group will join the "AKB48 Group Asia Festival 2019" event on January 27, 2019 at Impact Arena, Muang Thong Thani, Bangkok, Thailand after BNK48's 6th Single Senbatsu General Election. MNL48 will perform with their sister groups AKB48, JKT48, BNK48, AKB48 Team SH, AKB48 Team TP and SGO48. MNL48 members Abby, Brei, Coleen, Faith, Gabb, Jem, Mari, Rans, Sela and Sheki went to the event. On December 14, it was announced that MNL48 will be having their first mini-concert at Movie Stars Cafe, Centris Station, Quezon Ave on December 23, 2018.
On December 21, MNL48 released "Amazing Grace" music video with MNL48 Gospel unit members Sheki, Belle, Brei, Rans, Faith and Aly. The single was digitally released on December 24, 2018.
On January 26, the group performs for the first time outside the country at the "AKB48 Group Asia Festival 2019" event on January 27, 2019 at Impact Arena, Muang Thong Thani, Bangkok, Thailand after BNK48's 6th Single Senbatsu General Election. MNL48 performed with their sister groups AKB48, JKT48, BNK48, AKB48 Team SH, AKB48 Team TP and SGO48. On February 10, they unveil the music video of the second coupling song from "Pag-ibig Fortune Cookie", "Palusot Ko'y Maybe" as a tagalized version of AKB48's Iiwake Maybe which was performed by Team NIV and Coleen selected as the center girl of the said team's song. On February 22, MNL48 conducts a casting for 2nd generation to take part in the upcoming General Election. On March 1, 2019, they released a 3rd single, "365 Araw ng Eroplanong Papel". On March 25, the 20 members from the 2nd Generation were selected. On April 6, they held their concert at the New Frontier Theater (formerly Kia Theater) near Araneta Coliseum where its tickets were confirmed sold out through their bookings and/or reservations.
On April 27, the group celebrates its 1st anniversary back-to-back with the 2nd General Election where all 77 members over 2 generations competing for Top 48 spots. On the said event, the members who did not make it to Top 48 will immediately graduate from the group. 16 First Generation members (including Cassandra Mae Pestillos, Ella Mae Amat, Eunys Abad, Guinevere Muse, Hazel Joy Marzonia, Jessel Montaos, Khyan Jewel Cacapit, Madelaine Epilogo, Necca Adelan, Princess Erica Sanico, Princess Rius Briquillo, Sharei Engbino, Edelvira Bandong, Jamela Magbanlac, Polaris Yna Salazar, Ruth Carla Dela Paz) and 13 Second Generation members (including Abbigail Shaine Reyes, Alexie Iris Dimaayo, Alyssandra Corteza, Anne Nicole Casitas, Christina Samantha Tagana, Chrisylle Joy Mondejar, Francese Therese Pinlac, Missy Ainza, Naomi Roniele De Guzman, Je-ann Benette Guinto, Karla Jane Tolentino, Shay Anne Enciso, Trisha Labrador) were eliminated in the Second General Election with the 12 remaining trainees (5 from first generation & 7 from second generation) as the replacement of 12 first generation promoted members who outranked in the said event. Team NIV's Jhona Alyannah Padillo hailed as Shekinah Arzaga's successor as the "Center Girl" of the group. On May 1, MNL48 held an annual graduation event for 29 outranked members in the Second General Election (which consists of 12 first generation members, 4 first generation trainees and 13 second generation trainees) at Movie Stars Cafe at Quezon City to showcase their talents for one last time.
To fill-in the 12 empty spots from Top 48, 6 trainees were promoted to Team MII, 3 to Team NIV and 3 to Team L. Cole, Yzabel, Emz, Jamie, Klaire & Laney were promoted to Team MII, Dani, Rowee and Miho were promoted to Team NIV and Amy, Yssa & Ice were promoted to Team L.