The leading national "modernist" social organization, Muhammadiyah, has branches throughout the country and approximately 30 million followers. Founded in 1912, Muhammadiyah runs mosques, prayer houses, clinics, orphanages, poorhouses, schools, public libraries, and universities. On February 9, Muhammadiyah's central board and provincial chiefs agreed to endorse the presidential campaign of a former Muhammadiyah chairman. This marked the organization's first formal foray into partisan politics and generated controversy among members.

Nahdlatul Ulama (NU), the largest "traditionalist" social organization, focuses on many of the same activities as Muhammadiyah and indirectly operates a majority of the country's Islamic boarding schools. Claiming approximately 40 million followers, NU is the country's largest organization and perhaps the world's largest Islamic group. Founded in 1926, NU has a nationwide presence but remains strongest in rural Java. The Islam of many NU followers has heavy infusions of Javanese culture, and followers tend to reject a literal or dogmatic interpretation of Islamic doctrine. Many NU followers give great deference to the views, interpretations, and instructions of senior NU religious figures, alternately called "Kyais" or "Ulama." The organization has long advocated religious moderation and communal harmony.

The Indonesian Islamic Propagation Institute (LDII) has long been misunderstood by many Indonesians, with the enormous amount of black propaganda launched against them. Nevertheless, the number of the adherers of this organization continue to grow (Wakhid Sugiyarto, Kajian tentang Proses Santrinisasi ). LDII has a bi-monthly magazine named Nuansa Persada that includes a lot of news about activities and/or events that have been held by its adherers.

A number of smaller Islamic organizations cover a broad range of Islamic doctrinal orientations. At one end of the ideological spectrum lies the controversial Islam Liberal Network (JIL), which aims to promote a pluralistic and more liberal interpretation of Islamic thinking. Equally controversial are groups at the other end of this spectrum such as Hizbut Tahrir Indonesia (HTI), which advocates a pan-Islamic caliphate, the Indonesian Mujahedeen Council (MMI), which advocates implementation of Shari'a as a precursor to an Islamic state, and the sometimes violent Front Pembela Islam (FPI). Countless other small organizations fall between these poles.

Separate from the country's dominant Sunni Islam population, a small minority of persons subscribe to the Ahmadiyah interpretation of Islam. However, this group maintains 242 branches throughout the country. In 1980 the Indonesian Council of Ulamas (MUI) issued a "fatwa" (a legal opinion or decree issued by an Islamic religious leader) declaring that Ahmadiyah is not a legitimate form of Islam.

In addition there are small numbers of other messianic Islamic groups, including the Malaysian-affiliated Darul Arqam, and the syncretist Indonesian Jamaah Salamulla group (also called the Salamulla Congregation or The God's Kingdom). Its leader, Lia Eden, is currently facing charges of disdaining Islam and many Islamic organizations in Indonesia consider them as a heretic form of Islam.