阿赫迈底亚派穆斯林最早传入印尼是在1925年夏天（大约是在印尼独立革命前20年），由这个派别的传教士拉赫马特·阿里 (Rahmat Ali) 进入苏门答腊岛，在亚齐的塔帕克团（英语：Tapaktuan）开始活动，初期有13名信众 。[50]这个教派在印尼的宗教发展中曾发挥过影响力，但在现代却为其他伊斯兰教机构所不容，甚至激进穆斯林团体会对这个派别采取暴力行为。[50]估计阿赫迈底亚派组织（印尼阿赫迈底亚社团（印尼语：Jamaah Muslim Ahmadiyah Indonesia）(JMAI) 中有400,000名追随者，相当于印尼穆斯林人口的0.2%，[7]分布在全国542个分支组织；但印尼宗教事务部（英语：Ministry of Religious Affairs (Indonesia)）估计，这个教派的跟随者仅约有80,000名，与独立人士估计不同。[50]印尼另有一个阿赫迈底亚派的分离主义团体 - 拉合尔阿赫迈底亚伊斯兰传播运动（Lahore Ahmadiyya Movement for the Propagation of Islam），在印尼被称为 印尼语：Gerakan Ahmadiyah-Lahore Indonesia (GAI)，自1924年以来即存在于爪哇，到1980年代只有708名跟随着。[50]
天主教在14世纪和15世纪，因葡萄牙人到印尼群岛做香料贸易而传入当地。其中许多葡萄牙人的目标就是传播天主教，首先在1534年从摩鹿加群岛开始。传教先驱圣方济·沙勿略在1546年至1547年间遍访群岛中各岛屿，为数千名当地人施洗。在VOC统治印尼的时期，天主教受到禁止，天主教徒的数量显著下降。荷兰人对天主教的敌意有其历史上的原因，荷兰人信仰新教，他们经过八十年战争最终从信仰天主教的宗主国西班牙取得独立。VOC加大力度在佛洛勒斯岛和帝汶东部施加限制，导致天主教徒数目很显著的减少。天主教神父受到监禁或处以刑罚，并由荷兰派来新教神职人员取代。在17世纪，扬·彼得斯佐恩·库恩担任荷属东印度总督期间，有位天主教神父因为在狱中举行弥撒（英语：Mass in the Catholic Church）而遭到处决。VOC在18世纪末破产后，荷兰天主教于1800年左右再度合法化，此后荷兰天主教神职人员一直主导在印尼的传播事务，直到印尼独立为止。[52][59]在16世纪的弗洛勒斯岛上，曾建有一拉兰图卡王国（英语：Kingdom of Larantuka），是东南亚唯一由原住民所建立的天主教王国，第一位国王名叫洛伦佐（Lorenzo）。[60]
截至2018年，印尼人中天主教徒的占比为3.12%，数目接近新教徒占比（7.6%）的一半。[62]信徒大多居住在西加里曼丹省、巴布亚省和东努沙登加拉省。弗洛勒斯岛和西帝汶岛所在的东努沙登加拉省是印尼唯一天主教徒占多数的省份（约占总人口的54.14%）。在爪哇岛，天主教除爪哇族外，也传播到印尼华人。[52][63]在今天的佛洛勒斯岛，仍然在接近复活节时会举办天主教传统庆典，当地人称之为圣周（印尼语：Semana Santa）。仪式包括游行队伍将耶稣和圣母玛利亚（当地分别称为印尼语：Tuan Ana和印尼语：Tuan Ma）的雕像带到当地海滩，然后前往天主教拉兰图卡教区的圣母玫瑰主教座堂（Cathedral of the Queen of the Rosary）。[64]
印尼的印度教具有与其他地区不同的基调。[68][69]印尼把印度教称为Agama Hindu Dharma（Agama为宗教之义，Dharma为梵语，有哲学上的“法”之义），也采行种姓制度。[70]也把南岛民族的信仰元素如崇敬香、神祇、自然神灵和已故祖先融入。并透过印尼哇扬皮影偶戏和舞蹈把印度教的宗教史诗《摩诃婆罗多》和《罗摩衍那》情节演出。在印尼的各派印度教信仰者都有许多共同信仰，印度教主要的5个基本信仰（称为Panca Srada），包括对一位全能上帝（梵，宇宙的超越本体和终极实在）的信仰，对灵魂和无数地方和祖先神灵和业力的信仰（对互惠行为法则的信仰，而非对重生和转世的信仰）。此外，印尼印度教更注重艺术和仪式，而非宗教经典、法律和信仰。[68][71]在爪哇岛的许多地区，印度教和伊斯兰教相互间有巨大影响，是导致阿邦甘（英语：Abangan）（保留当地信仰的爪哇伊斯兰教徒，也称为“名义上的”穆斯林）和科贾文信仰传统发生的部分原因。[72]
在苏卡诺总统于1960年代中期卸任之后，印尼建国五原则（Pancasila）被重申为印尼的官方宗教政策，而此政策只承认一神论。[78]结果是Perbuddhi（印尼佛教组织（Indonesian Buddhists Organisation））创始人体正老和尚（英语：Ashin Jinarakkhita）（印尼出生华人后裔，俗名Tee Boan-an[79]戴满安）提出佛教有一至尊之神，即成佛种子（英语：Sanghyang Adi Buddha）（印尼语：Sanghyang Adi Buddha）。他还以古爪哇语（英语：Kawi）中撰写的佛教经典相关历史以及婆罗浮屠寺庙来支持其立论。[80]
根据新加坡作者与政治家李炯才的看法，Kejawèn没特定的先知、[91]圣书，[91]也没有独特的宗教节日和仪式；这种信仰更多地与每个追随者内化的超验视野和信仰，及他们与他人和至高无上神灵的关系有关。因此这些信仰者可在身份证中注明为为6种官方认可的任何一种，但仍依循Kejawèn信仰和生活方式。这种组织松散的思想和信仰潮流在1945年的宪法中有合法地位，并在1973年被承认为尊崇一位至高无上的上帝信仰（印尼语：Kepercayaan kepada Tuhan Yang Maha Esa），在某种程度等同取得合法宗教的地位。前总统苏哈托即自诩为这种信仰的拥护者。[92]
修菩达由穆罕默德·苏布·苏墨哈迪维多多（英语：Muhammad Subuh Sumohadiwidjojo）在1920年代创立。 而修菩达这个名字在1940年代后期，当团体经合法注册后才开始使用。修菩达运动的基础是倡导修行，通常被称为灵性修行（英语：latihan）（印尼语：latihan kejiwaan），苏墨哈迪维多多将其称为“上帝的力量（the Power of God）”或“伟大的生命力量（the Great Life Force）”的指导。 苏墨哈迪维多多的目标是依循上帝的旨意达到完美的品格。[94]只有激情、心思和意念与内心的感觉能够分开时，才能接触到无处不在的“伟大的生命力量”。[95][96][97]
锡克教徒于1870年代开始移民到印尼（商人，及担任警卫者）。苏门答腊岛和爪哇岛有几所谒师所和学校，例如有一处建于棉兰（1911年）。印尼锡克教最高委员会（Supreme Council for the Sikh Religion in Indonesia）在2015年成立。[112]印尼的锡克教信徒约有7,000人（另称介于10,000至15,000人之间[7]），由于这个宗教并未得到政府正式承认，导致信徒在身份证上注明自己为印度教徒。[113]
印尼政府透过提出宗教间合作计划，努力缓和紧张局势。印尼外交部与印尼最著名的伊斯兰组织伊斯兰教士联合会共同举行国际伊斯兰学者会议（International Conference of Islamic Scholars），以倡导伊斯兰温和主义（英语：Moderation in Islam）（wasat ），据信可因此缓解印尼国内的紧张局势。[127]“宗教间合作对话：社区建设与和谐”会议于2004年12月6日举行。亚细安国家、澳大利亚、东帝汶、新西兰和巴布亚新几内亚均派代表参加这次会议，以讨论不同宗教团体之间的合作，尽量减少印尼宗教间的冲突。[127]
Statistik Umat Menurut Agama di Indonesia. Kementerian Agama Republik Indonesia. 2018-05-15 [2020-11-15]. （原始内容存档于2020-09-03） （印度尼西亚语）. Muslim 231 Million (86.7), Christian 20.45 Million (7.6), Catholic 8.43 million (3.12), Hindu 4.65 million (1.74), Buddhist 2.03 million (0.77), Confucianism 76.630 (0.03), Others/Traditional faiths 126.51 (0.04), Total 266.5 Million
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C.I.C.R.E.D. cites SUSENAS TAHAP KEEMPAT – Sifat Demografi Penduduk Indonesia [National Survey of Social and Economic Fourth Round – Demographic Characteristics of the Population]. Jakarta: Biro Pusat Statistik (Central Bureau of Statistics). 1969. for Table III.10 of "The Population of Indonesia, 1974 World Population Year", p. 31. However, due to inaccessibility of the data source for verification and data collection proximity to census year 1971, referenced 1969 data is not included in this article's table. The Population of Indonesia, 1974 World Population Year(PDF). C.I.C.R.E.D. 2. Jakarta: Lembaga Demografi (Demographic Institute), Universitas Indonesia. 1973: 31–32 [2018-01-18]. LCCN 77366078. OCLC 3362457. OL 4602999M. （原始内容存档(PDF)于2016-10-21）. The statistical data on religion show that Islam has the highest percentage of adherents with about 87.1 per cent of the population of Indonesia (National Socio Economic Survey, 1969). The second biggest religion in Indonesia is Protestant (5.2%), while Catholic is the third (2.5%). The rest are Hindu (2.0%) and Buddhist (1.1%) and other religions which are not included in the above classification.
Unable to find online data for Sensus Penduduk 1980 (Penduduk Indonesia: hasil sensus penduduk. Jakarta: Badan Pusat Statistik, 1980). Unable to find online version of Buku Saku Statistik Indonesia 1982 [Statistical Pocketbook Of Indonesia 1982]. Jakarta, Indonesia: Biro Pusat Statistik. 1983. OCLC 72673205., which contains 1980 census data.
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The 1990 census recorded 87.21% Muslims, 6.04% Protestants, 3.58% Catholics, 1.83% Hindus, 1.03% Buddhists and 0.31% as "Others". Population of Indonesia: Results of the 1990 Population (Jakarta: Biro Pusat Statistik, 1992), p. 24, as cited by
Indonesia. The World Factbook. Washington, D.C.: U.S. Central Intelligence Agency. People and Society. 2011-10-18 [2011-11-08]. ISSN 1553-8133. （原始内容存档于2021-04-13）. Muslim 86.1%, Protestant 5.7%, Roman Catholic 3%, Hindu 1.8%, other or unspecified 3.4% (2000 census)
In 1979, Soeharto retracted official recognition of Confucianism. Hence Confucianism appears in the 1971 census data, but not in 1980 or 1990. In 2000, Indonesia decided to separately categorise Confucianism only during the enumeration process, but did not actually list this option on the printed form. This is not listed as a separate category in the U.N. data. Utomo, Ariane J. Indonesian Census 2000: Tables and Reports for AusAID Explanatory Notes(PDF) (报告). The Australian National University: 7. March 2003. （原始内容(PDF)存档于2012-04-25）. The six categories for religion were Islam, Catholicism, Protestant, Hinduism, Buddhism, and Other. The decision to have a separate category for Confucianism (Kong Hu Cu) occurred during the enumeration process itself, hence it was not printed in the actual form of the L1. The data on the number of Confucians is only available for certain provinces. However, the number seems much smaller than expected due to the abrupt process of including it in the questionnaire.
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