Quincy Josiah Santillan confirmed her resignation as part of Team L on May 23, 2019 and is replaced by Ella Mae Amat, a First Generation returning member and Sayaka Awane of Team MII announced her graduation on June 3 and she was replaced by Princess Rius Briquillo, a First Generation returning member.
On July 29, MNL48 released a new song "Ikaw ang Melody" as a translated version to AKB48's "Kimi Wa Melody".
On August 24, the group performed in Asia Festival Concert in Shanghai, China at the National Convention Centre along with overseas sister groups, and AKB48.
Ashley Cloud Garcia from Team L announced her graduation on September 4 and was replaced by "Kenkyuusei" Frances Therese Pinlac.
The group signed an exclusive contract with ABS-CBN on October 4, 2019 with K-pop girl group Momoland.
On October 19, it was announced that their 5th single will be "High Tension" and MNL48 Gabb of Team L will be the center.
On November 5, Princess Labay from Team MII committed several house rule violations that lead her to dismissal of membership from the group, who is then replaced by Guinevere Muse as part of Team MII.
On December 31, MNL48 Abby joined the AKB48 World Senbatsu along with other overseas sister groups and performed Koisuru Fortune Cookie. She is the third Filipino to perform in the annual NHK Kouhaku Uta Gassen after Smokey Mountain and Gary Valenciano.
On January 24, Hallo Hallo Entertainment decided to part ways with Daniella Mae Palmero of Team NIV due to violations. She was then replaced by Trainee Karla Dela Paz.
On January 25, MNL48 announces the 3rd Generation Audition to determine who will be promoted to Training and Development Team as candidates for 3rd year members. Its 3rd General Election's protocol will be followed through AKB48's General Election, and JKT48's Promotion-Demotion system. For those members who will be included in Top 48, they will be promoted to Teams MII, NIV & L, while for those who are outranked, they will be demoted to Training and Development Team. No force graduations applied as it was applied in the 2nd General Election.
On January 26, Team MII's Faith Shanrae Santiago had her graduation concert at Movie Stars' Cafe. "Kenkyuusei" Christina Samantha Tagana joined as her replacement.
On February 19, the official music video for "High Tension" was premiered on the group's official YouTube channel.
In lieu with the ongoing COVID-19 crisis, MNL48 joined its 48G counterparts and other well-known Asian performers in a charity show called "One Love Asia", presented by YouTube and WebTVAsia, supported by UNICEF on May 27.
On February 16, the group held the Valentine Mini Concert at Movie Stars Cafe. In the midst of the concert, it was announced that the 6th single will be "River". Gabb and Abby will be the first double centers in a MNL48 single.
On June 10, at MNL48 Kumu livestream, over-all captain Alice announced that she will join the Senbatsu for "River" as replacement of Rans.
On November 11, MNL48 released a teaser video for the latest single, "River". Due to undesirable calamities in the Philippines, the HHE management released a statement that the music video will be postponed. On November 27, MNL48 premiered the official music video of "River". The coupling tracks "Sampung Taon ng Sakura" and "Labrador Retriever" were also released on iTunes, Apple Music and as auto-generated tracks in YouTube Music the same day.
On March 12, MNL48's Team NIV performed "1! 2! 3! 4! Yoroshiku" at audience-free "It's Showtime", and they announced that the 3rd General Election will be aired at the said program on April 25. Due to COVID-19 pandemic in the Philippines, the voting lines for General Election were extended until October 31. On March 15, the candidates for the 3rd General Election was announced, consisting of 62 candidates (44 from first and second generation, 2 from "Kenkyuusei," and 16 from third generation). Eligible candidates Rans, Yssa, Lei, and Rowee will not join the Third General Election due to personal reasons. On March 24, 3rd generation aspirant Querubin Gonzalez withdrew the candidacy for official 48 members. Two days later, former "" housemate Jelay Pilones joined the candidacy for the 3rd General Election.
On May 18, in the midst of the voting process, Team NIV's Valerie Joyce Daita will no longer to join the 3rd General Election due to her personal reason. Eleven days after, Yiesha Amera Ungad also resigned her candidacy from the group with regards to her religion as a Muslim.
On June 22, Daryll Matalino withdrew her candidacy in the upcoming General Election to finish her project as an actress on "MNL48 Presents: Chain", following her graduation announcement.
On August 4, the remaining 2nd Generation "Kenkyuusei" Anne Nicole Casitas and Trisha Labrador promoted as official members of MNL48 as part of Team NIV.
On September 30, Team NIV Captain Ecka Sibug announced her withdrawal from the Third General Elections and the MNL48 group itself. The same day, MNL48 posted on their official Facebook page that HalloHallo Entertainment (HHE) has decided that for the Third General Elections, the group will become a 36-member girl group, in order to focus more on individual projects and sub-units HHE has slated for the next months.
On October 28, three days before the voting deadline, HHE released a statement that the Third General Election will be announced very soon. On the other hand, the voting period will be extended until November 30. On November 28, Team NIV's Belle delos Reyes withdrew her candidacy to complete the music video of "River", leaving the 56 official candidates of the Third General Election.
On November 29, the first preliminary results of the Third General Election was released as of November 28, 6 p.m. PST. First Generation center Sheki leads for center position. Followed by Andi, Ruth, Coleen, Ella, Jem, and Jamie for Kami 7. The first preliminary Top 36 consists of 11 members from Team MII, 10 from Team NIV, 10 from Team L, and 5 from Third Generation aspirant. Few hours after the preliminary result, top member Sela Guia formally announced her graduation. On November 30, few hours before the voting cutoff, the second preliminary results was released as of November 29, 10:30 p.m. PST. Abby overtakes Sheki for the center spot. Followed by Andi, Ruth, Jem, Coleen, and Ella are now in Kami 7. The second preliminary top 36 consists of 11 members each from Team MII and Team NIV, 10 from Team L, and 4 from Third Generation aspirant.
On September 1, MNL48 announced the formation of BABY BLUE, the group's first-ever sub-unit, in partnership with Tower Records Japan, a major Japanese music retailer. Said sub-unit is formed by MNL48 members Jan Elaurza, Coleen Trinidad and Amy Isidto. Following the announcement, BABY BLUE officially released its debut single titled "Sweet Talking Sugar", and was made available through EGGS, a Japanese digital music subscription service. The single, according to HHE, is an homage to the famed city pop genre, with a modern take via "the R&B and hip-hop genre". An official music video, produced by Carlo Manatad of Plan C, was released on GYAO!, Yahoo Japan's free online streaming site on September 16 and on MNL48's official YouTube channel on the next day.
A second track, "NEGASTAR" was released by the sub-unit officially after they uploaded a sixty-second teaser uploaded on the music subscription service EGGS on November 16. The full track was then uploaded on November 25 and was also made available on mainstream music streaming platforms like iTunes and Spotify.
On December 23, MNL48 premiered its first-ever original song called "HASHLOVE", a pop/R&B song centered around the theme of Christmas celebrations. The track was performed by select members namely Shekinah Arzaga, Frances Pinlac, Cole Somera, Jamie Alberto, Yzabel Divinagracia, Ruth Lingat and Brei Binuya. "HASHLOVE" is composed by Filipino music producer Jungee Marcelo.