The UST Lady Booters joined the inaugural five-team UAAP Women's football tournament that began on November 30, 1995.
The Lady Booters reached the Finals again in Season 65 but fell short against La Salle for the second time, surrendering a wide margin of 1–5.
Joyce Landagan scored the lone goal for the Lady Booters to prevent a shutout by the eventual champions.
Moving on from the team with the former coach were their leading scorers, Alelie Bonifacio who has used up her five-year playing eligibility; and Landagan who was left out of the roster due to academic deficiencies.
[10] With La Salle's suspension in Season 69 and having to contend with only three other teams, UST reached the Finals again but became unsuccessful yet again when they lost the title to FEU.
The following year gave the Lady Booters an auspicious start, having finally won the UNIGAMES and the Metro Manila Girls Football Association crowns in the offseason.
[11] Bejemino stepped down in 2008 and was replaced by Bon Estrabon who went on to lead the team to their first UAAP women's football title in Season 71.
Narciso, who was also held scoreless by their opponents, received the Best striker award with a season-high total of nine goals scored in the tournament.
[13][14] After a back-to-back Finals affair with La Salle, the Lady Booters once again faced FEU after topping the eliminations with a 5–1–2 win–draw–loss record.
FEU had a chance to equalize in the second half when a UST defender was called for a handball violation, but Kristia Sabanal missed the penalty when her shot bounced off the post.
Marianne Narciso was again named Best striker with four goals scored in the season, and Pearl Anjanette Aguilar was given the Rookie of the year award.
The Lady Booters held a twice-to-beat advantage, but their opponents forced a deciding game with a 4–3 penalty shootout win.
The Lady Booters began Season 76 on a goalless draw with Ateneo, with Judal attributing the outcome to inexperience by the team's many rookies.
Charisa Lemoran and Shelah Cadag scored two goals apiece with Mary Joy Indac adding a fifth for the match.
Carmela Sacdalan, who replaced the already-graduated Nicole Reyes as the team's goalkeeper, failed to stop the penalty goal from UP's Stacey Arthur in the 35th minute.
They ended the tournament at fifth place after seven matches, defeating UAAP rivals FEU and Ateneo, as well as getting a big win against Stallion FC, with a 9–0 score.
[33][34][35][36] UST ended UAAP's Season 85 tournament ranked fourth out of the five-team field with three wins against four losses and a draw.
It was only slightly better than their 2016 season during Coach Aging Rubio's first year with the Lady Booters, where they also finished last, winning also only a single match against a draw and six defeats.
Another factor that the long-tine coach cited was their lack of training, which was caused by the ongoing reconstruction of the UST Open Field.
[41][42] Earlier in the 2023 PFF Women's League, the Lady Booters ended up at eighth place in the ten-team tournament, after beating Stallion FC, 5–2 on a 2–6–1 win–loss–draw record.
[43] Long-time Golden Booters head coach Marjo Allado replaced Aging Rubio in July 2024.
Allado's appointment to the team posed some challenges, with the football tournament set to begin in the first semester of the school year and leaving them little time to adjust and prepare under a new coaching system.
The change in the tournament's schedule was brought about by the extreme hot weather condition that they experienced earlier in the year, in the concluded previous season.
The team made a turnaround in the second round, first, by securing a draw against second-running La Salle, and then blanking Ateneo, 3–0.
As of 21 Sep 2024 Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.