Indonesia Liga 1

In 1994, PSSI merged the existing Perserikatan and Galatama to form Liga Indonesia. This decision was taken to increase the quality of Indonesian football. In order to do so, PSSI sought to combine supporter's fanaticism from Perserikatan and Galatama's professionalism. The Premier Division was the first-tier in Liga Indonesia. The system stayed put until 2007.

In 2008, PSSI formed the Indonesia Super League (ISL), the first fully professional league in Indonesia, as the new top-tier of Indonesian football. The Premier Division was then being relegated to the second-tier.

The modern competition era started in 2008 with the 2008–09 Indonesia Super League. The first season began with 18 clubs. The first Indonesia Super League goal was scored by Ernest Jeremiah of Persipura in a 2–2 draw against Sriwijaya F.C. The 18 inaugural members of the new Indonesia Super League were Persipura, Persiwa, Persib, Persik, Sriwijaya, Persela, Persija, PSM, Pelita Jaya, Arema, Persijap, Persiba, PKT Bontang, Persitara, PSMS, Deltras, Persita, and PSIS. Originally, Persiter and Persmin qualified to register but they failed the verification requirements to be inaugural members of the Indonesia Super League.

As the football scene in Indonesia was heavily politicized with rival factions upending each other, conflict was the norm prior to 2017. The worst conflict occurred in 2011. After the inauguration of the new PSSI board in 2011, a member of PSSI's Executive Committee and chairman of its Competition Committee, Sihar Sitorus, appointed PT Liga Prima Indonesia Sportindo as the new league operator replacing PT Liga Indonesia because LI failed to provide an accountability report to the PSSI. Sitorus, one of many politicians in the PSSI, announced the Indonesia Premier League as the new top-level competition in Indonesia. Upon the emergence of Liga Primer Indonesia (LPI), PSSI did not recognize the validity of ISL. ISL regulars PSM, Persema, and Persibo, which had boycotted the ISL operators due to referee and management decisions, gladly defected to join LPI along with splinters of existing ISL teams. However, the 2011 LPI season was stopped mid-season, due to continued schism within PSSI; a new league, Indonesian Premier League (Liga Prima Indonesia, IPL) replaced it in late 2011 for the 2011–12 season.

Before the schism of PSSI, Sitorus triggered more controversy when he said the new competition would be divided into two regions and there would be an addition of six clubs in the top division, which angered many association members. Thus, 14 teams that were supposed to be Indonesia Premier League contestants chose to support the Indonesia Super League that continued to roll under the support of the pro-IPL faction, despite being labeled as an illegal competition. The official PSSI, supported by FIFA and AFC, did not recognize the ISL for two seasons. In the meantime, the Indonesian Premier League became the top-tier league from 2011 to 2013 with only 11 teams.

In a PSSI extraordinary meeting on 17 March 2013, association members slammed Sitorus and decided that the Indonesia Super League would once again emerge as the top-level competition, following the disbandment of the Indonesian Premier League. Sitorus and five other PSSI board members were suspended from the sport for their roles in the split (locally referred to as dualisme, lit. 'dualism') that disrupted Indonesian football.

The new PSSI board also decided that the best seven teams of the 2013 Indonesian Premier League, following verification, would join the unified league. Semen Padang, Persiba Bantul, Persijap, and PSM passed verification, while Perseman, Persepar, and Pro Duta did not, meaning the 2014 season was contested with 22 teams.

The impact of split haunted Indonesian football years after the reconsolidation. On 18 April 2015, Minister of Youth and Sports Affairs Imam Nahrawi officially banned the activities of PSSI after PSSI refused to recognize the recommendations from the Indonesian Professional Sports Agency (Badan Olahraga Profesional Indonesia; BOPI), an agency under the ministry, that Arema Cronus and Persebaya should not pass ISL verification because there were still other clubs using the same name. Previously, Nachrawi had sent three letters of reprimand. However, PSSI refused to answer his call until a predetermined deadline. As a result, PSSI officially stopped all competitions in 2015 season after PSSI's Executive Committee meeting on 2 May 2015 called the government intervention as a force majeure.

The government intervention also led FIFA to punish Indonesia with a one-year suspension of all association football activities as the world body considered overbearing state involvement in footballing matters as a violation against its member PSSI. During the suspension, some tournaments were made to fill the vacuum, starting with the 2015 Indonesia President's Cup, in which Persib came out as champions, until the Bhayangkara Cup closed the series of unrecognized tournaments.

On 13 May 2016, FIFA officially ended the suspension, following the revocation of the Indonesian ministerial decision on 10 May 2016. A long-term tournament with full competition format, Indonesia Soccer Championship, emerged shortly thereafter. The 2016 season saw Persipura take the title.

In 2017, the top-flight football competition was rebranded under a new official name, Liga 1. The name changes also applied to Premier Division (became Liga 2) and Liga Nusantara (became Liga 3). The operator of the competition was also changed from PT Liga Indonesia (LI) to PT Liga Indonesia Baru (LIB). Bhayangkara was the first champion of the competition under the new name in the 2017 season. True to the controversial nature of Indonesian football, the crowning triggered flak from fans. Bhayangkara, a team managed by the Indonesian Police that had no fanbase, won due to head-to-head advantage against Bali United, a team with rapidly growing support due to its modern professional management, after both teams had the same points at the end of the season. Bali United finally won the title in 2019, the year after Persija.

The 2020 season was canceled as the COVID-19 pandemic began to hit Indonesia. The 2021–22 season used the bubble-to-bubble system so that it would not become a new cluster for the spread of COVID-19. The 2022–23 season was marred by the Kanjuruhan Stadium disaster and was finished without relegation. The 2023–24 season introduced the championship play-off after the regular season. The 2024–25 season sees at least one team represent each island in the league.