這項傳教活動取得巨大成功，並得到德國教會大力支持，傳教士採用的是德國傳教士路德維希·英格威爾·諾門森（英语：Ludwig Ingwer Nommensen）的有效佈道策略。諾門森從1862年到1918年在當地度過其人生大部分時間，成功讓許多司馬輪貢族（英语：Simalungun people）和多巴巴塔克族（英语：Toba Batak people）（也包含少數安克拉族）皈依。諾門森最初建立“和平村” （Huta Dame）以收容信仰基督教而被家人驅逐者，他也因此而對巴塔克人的習俗瞭如指掌。繼諾門森的成功，另一傳教士彼得約翰森（Peter Johannsen）於1866年抵達，他的巴塔克語翻譯品質優良，受到眾人以及當地受人尊敬的早期皈依者 - 巴塔克地方領袖 (Batak Raja Pontas) 的讚譽。諾門森的佈道方式是把基督教視為對巴塔克人習俗的更新，而非取代，但當地習俗與基督教信仰發生直接衝突時，則作例外處理。巴塔克基督教新教教會（英语：Batak Christian Protestant Church）（印尼語：Huria Kristen Batak Protestan（簡稱HKBP）是諾門森努力經營而形成的教會。為滿足當地對教育的渴望，教會在基督教村莊建立神學院和小學。到1918年諾門森去世時，HKBP的成員已達180,000人，擁有34名牧師和788名教師/傳教士。
第一次世界大戰和第二次世界大戰後，去殖民化持續進行，HKBP也繼續成長，不僅在巴塔克人土地，也進入爪哇島和棉蘭，因為許多巴塔克人去那裡參與經濟活動。這個教會在1951年至1960年間，會眾增長50%，達到745,000人。在HKBP中，其他亞群對多巴巴塔克族佔優勢的“帝國主義”日益不安，而導致在1960年代有司馬輪貢基督教新教教會（英语：Gereja Kristen Protestan Simalungun）和安克拉基督教新教教會（Gereja Kristen Protestan Angkola）的設立，這兩者都是當地的司馬輪貢族和安克拉族語言和傳統運動的表達。到1992年，帕克帕克族（英语：Pakpak people）也成立帕克帕克基督教新教教會，而脫離HKBP。
第一次世界大戰後，禮賢會的傳教工作被來自瑞士的崇真會所取代。崇真會於1935年把當地傳教工作移交給第一個獨立的教會“福音派達雅教會（Gereja Dayak Evangelis）”，這個教會覆蓋的區域廣大，從馬辰以西1,300公里到內陸600公里都包括在內。1950年，隨著印尼其他地區因印尼國內移民計畫而遷移到加里曼丹的移民加入為會眾，這個教會成為更具種族包容性的“福音派加里曼丹教會（Gereja Kalimantan Evangelis）”（GKE）。這個教會約有250,000名成員，總部設在中加里曼丹省。[31]
Blimbingsari村在1948年發展為巴厘島新教教會，稱為Gereja Kristen Protestan Bali（GKPB）。在GKPB的前身，以及本身早期，均遵循荷蘭歸正教會亨德里克·克里莫（英语：Hendrik Kraemer）提倡的神學，把大部分巴厘島文化視為異教和非基督，而予以摒棄，不用當地傳統的甘美朗樂團，而改用歐式銅管樂隊。結果是許多巴厘島新教徒選擇離開巴厘島，這類人在很大程度上被排除在巴厘島人的日常生活之外，以至於巴厘島以外的GKPB成員多於巴厘島上的數目。
葡萄牙人曾在北蘇拉威西省美娜多為一千多人施洗，葡萄牙人和基督教被視為可與在當地正東緊鄰的德那第蘇丹國對抗的力量。葡萄牙傳教活動在1563年至1570年間仍在當地西北部繼續進行，但隨著德那第蘇丹國蘇丹海潤（ Sultan Hairun）被葡萄牙人謀殺，以及之後蘇丹國反葡萄牙人戰鬥行動，傳教活動因而必須放棄。[45]
第二次世界大戰後，巴布亞仍由荷蘭政府控制（荷屬新幾內亞），但在1963年成為印尼國土。印尼政府對當地的“荷蘭”元素（包括教會學校以及傳教團）抱持懷疑態度，而立即展開印尼化的工作。透過國內移民計畫遷移大量穆斯林移民到巴布亞，印尼政府為移民提供土地和住房。由於宗教差異，以及當地人與信仰伊斯蘭教的印尼軍隊和政府行政人員間的文化差異而加劇衝突，導致數千名巴布亞人被安全部隊殺害。 根據國際原住民事務工作團（英语：International Work Group for Indigenous Affairs）（簡稱IWGIA） 等人權組織估計，遭到殺害的巴布亞人超過100,000人。[50]
根據一篇在2015年刊出的研究報告：“《來自穆斯林背景的基督信徒：全球人口調查（Believers in Christ from a Muslim Background: A Global Census study）》”，在1960年至2015年期間，約有650萬印尼穆斯林皈依基督教。[87]
一些報導還顯示，許多印尼華人皈依基督教。[88][89][90][91][92]人口統計學家阿里斯·阿南塔在2008年報導說，“軼事證據顯示，有越來越多信奉佛教的華人隨著教育水準的提高，而變為基督徒”。[16]根據澳大利亞國立大學的學者Gavin W. Jones[93]的說法，印尼“華人基督徒的數量迅速增長”，“在1960年代印尼華人皈依基督教的速率加快，特別是在東爪哇，華人在印尼天主教徒中的比例從1957年的2%，上升到1969年的6%”。[94]
^Aris Ananta, Evi Nurvidya Arifin, M Sairi Hasbullah, Nur Budi Handayani, Agus Pramono. Demography of Indonesia's Ethnicity. Singapore: ISEAS: Institute of Southeast Asian Studies, 2015. p. 273.
^ 2.02.1Statistik Umat Menurut Agama di Indonesia. Kementerian Agama Republik Indonesia. 2018-5-15 [2020-11-15]. （原始内容存档于2020-9-3） （印度尼西亚语）. Muslim 231.069.932 (86.7), Christian 20.246.267 (7.6), Catholic 8.325.339 (3.12), Hindu 4.646.357 (1.74), Buddhist 2.062.150 (0.77), Confucianism 71.999 (0.03), Others/Traditional faiths 112.792 (0.04), Total 266.534.836请检查|date=, |archive-date=中的日期值 (帮助)
^ 7.07.1Penduduk Menurut Wilayah dan Agama yang Dianut [Population by Region and Religion]. Sensus Penduduk 2010. Jakarta, Indonesia: Badan Pusat Statistik. 2010-05-15 [2011-11-20]. （原始内容存档于2018-12-24）. Religion is belief in Almighty God that must be possessed by every human being. Religion can be divided into Muslim, Christian, Catholic, Hindu, Buddhist, Hu Khong Chu, and Other Religion. Moslem 207176162 (87.18%), Christian 16528513 (6.96%), Catholic 6907873 (2.91%), Hindu 4012116 (1.69%), Buddhist 1703254 (0.72%), Khong Hu Chu 117091 (0.05%), Other 299617 (0.13%), Not Stated 139582 (0.06%), Not Asked 757118 (0.32%), Total 237641326
^Situation of ethnic Chinese Christians in Indonesia (2001–2003). Responses to Information Requests. Ottawa, Ontario: The Immigration and Refugee Board of Canada. 2003-12-9 [2012-2-15]. IDN42199.E. （原始内容存档于2012-9-5）. Approximately three per cent of Indonesia's population is ethnic Chinese [], most of whom are Christians[.]请检查|access-date=, |date=, |archive-date=中的日期值 (帮助)
^Directory Profile Aris Ananta. International Union for the Scientific Study of Population. [2022-7-20]. （原始内容存档于2022-09-05）.请检查|access-date=中的日期值 (帮助)
^Adolf Heuken. Ensiklopedi Gereja (2005). See Also Adolf Heuken, "Chapter One: Christianity in Pre-Colonial Indonesia", in A History of Christianity in Indonesia, eds. Jan Aritonang and Karel Steenbrink, pgs. 3–7, Leiden/Boston: Brill, 2008, ISBN978-90-04-17026-1
^History of Christianity in Indonesia. pp. 121–132
^History of Christianity in Indonesia. pp. 527–569
^ 34.034.1Gereja Kemah Injil Indonesia. reformiert online. [2022-7-22]. （原始内容存档于2022-03-31）. In 1939 Fisk was the first missionary in Indonesia to use a plane in the service of the mission, to overcome the difficulties of traveling in the jungle. The mission fields mentioned above were mainly inhabited by adherents to tribal religions, sometimes by Muslims (Lombok, Sumbawa) or Hindus (Bali).请检查|access-date=中的日期值 (帮助)
^History of Christianity in Indonesia. Chapter Fifteen
^Encyclopedia of Protestantism: 4-volume set by Hans J. Hillerbrand
^ 55.055.1David B. Barrett; George Thomas Kurian; Todd M. Johnson (编). World Christian Encyclopedia p.374. Oxford University Press USA. 2001-02-15. ISBN 0195079639.
^Miller, Duane Alexander; Johnstone, Patrick. Believers in Christ from a Muslim Background. Interdisciplinary Journal of Research on Religion (Waco, TX: Baylor University). 2015, 11 [2016-6-23]. ISSN 1556-3723. （原始内容存档于2021-03-13）. [A]ccurately estimating the number of such converts is very difficult [...] In Indonesia, a great number of new converts to Christianity occurred among the non-Muslim peoples of Indonesia and to an extent among the 'folk' Muslim East Javanese. The failed Communist coup of 1965, the subsequent massacres of supposed supporters of that coup by Muslims, and legislation that required all Indonesians to sign up for one of the five official religions of the country led to a huge turning to the Christian churches for refuge and engendered disgust for the cruelties perpetrated in the name of Islam.请检查|access-date=中的日期值 (帮助)
^Narciso, Jerson Benia. Christianization in New Order Indonesia (1965–1998). Melintas (Bandung, Indonesia: Parahyangan Catholic University). 2008-3-24, 24 (3): 407–428 [2016-6-23]. ISSN 0852-0089. OCLC 45613609. （原始内容存档于2022-09-05）. [T]he massive religious conversion of 1965 and onward should be understood against the backdrop of government pressures and policies which required all citizens to embrace an official religion. They also observe that some Indonesians decided to become Christian because they felt there had been too much tension between Islam and communism. Christianity perhaps was the least risky option.请检查|access-date=, |date=中的日期值 (帮助)
^Karel Steenbrink/Mesakh Tapilatu (2008), Moluccan Christianity in the 19th and 20th century between Agama Ambon and Islam, in: Jan Sihar Aritonang/Karel Steenbrink (eds.), A history of Christianity in Indonesia. Leiden: Brill, p. 414
^Bresnan, John. Indonesia: The Great Transition. Rowman & Littlefield. 2005: 107. ISBN 9780742540118. Between 1966 and 1976, almost 2 million ethnic Javanese, most from nominally Islamic backgrounds, converted to Christianity. Another 250,000 to 400,000 became Hindu.
^P. Daniels, Timothy. Sharia Dynamics: Islamic Law and Sociopolitical Processes. Springer. 2017: 102. ISBN 9783319456928. almost two million nominal Muslims to convert to Christianity
^Madan, T. N. Sociological Traditions: Methods and Perspectives in the Sociology of India. SAGE Publications India. 2011: 53. ISBN 9788132107699. Simultaneously, a considerable number of muslims (about 2 million) converted to Christianity and Hinduism, a most unique event.
^L. Berger, Peter. The Limits Of Social Cohesion: Conflict And Mediation In Pluralist Societies. Routledge. 2018: 53. ISBN 9780429975950. Some 2 million nominally Islamic Javanese reacted against the violence of their Muslim brethren by converting to Christianity
^Religion and Education in Indonesia(PDF). Gavin W. Jones. 2017-1-30 [2022-09-10]. （原始内容存档(PDF)于2021-07-19）. Finally, during this century there has been a rapid growth in the number of Chinese Christians. Very few Chinese were Christians at the turn of the century. Today Christians constitute approximately 10 or 15 percent of the Chinese population in Indonesia, and probably a higher percentage among the young. Conversion of Chinese to Christianity accelerated in the 1960s, especially in East Java, and for Indonesia as a whole the proportion of Chinese who were Catholics rose from 2 percent in 1957 to 6 percent in 19.请检查|date=中的日期值 (帮助)
^Religion and Education in Indonesia(PDF). Gavin W. Jones. 2017-1-30 [2022-09-10]. （原始内容存档(PDF)于2021-07-19）. P.25: Finally, during this century there has been a rapid growth in the number of Chinese Christians. Very few Chinese were Christians at the turn of the century. 22 Christians today make up roughly 10 or 15 percent of the Chinese population in Indonesia, 23 and perhaps a higher proportion among the young. The conversion of Chinese to Christianity accelerated in the 1960s, particularly in East Java, and for Indonesia as a whole, the proportion of Chinese who were Catholic rose from 2 percent in 1957 to 6 percent in 1969 (24). locally born) Chinese. This growth appears to be a response to intense missionary efforts and a search for acceptance and identity in Indonesian society through the adoption of a more acceptable and less "Chinese" religion25 which at the same time removes suspicion of sympathy with the communists.请检查|date=中的日期值 (帮助)
