| Teologi pluralis multikultural: menghargai kemajemukan, menjalin kebersamaan M Ali Penerbit Buku Kompas, 2003 | 288 | 2003 |
| Kajian Naskah dan kajian living Qur’an dan living hadith M Ali Journal of Qur’an and Hadith Studies 4 (2), 147-167, 2015 | 101 | 2015 |
| The understanding of Islamic Moderation (wasatiyyah al-Islam) and the hadiths on inter-religious relations in the Javanese pesantrens MI Helmy, ADJ Kubro, M Ali Indonesian Journal of Islam and Muslim Societies 11 (2), 377-401, 2021 | 77 | 2021 |
| Muslim diversity: Islam and local tradition in Java and Sulawesi, Indonesia M Ali Indonesian Journal of Islam and Muslim Societies 1 (1), 1-35, 2011 | 74 | 2011 |
| Islam and colonialism: Becoming modern in Indonesia and Malaya M Ali Edinburgh University Press, 2015 | 73 | 2015 |
| The rise of the Liberal Islam Network (JIL) in contemporary Indonesia M Ali American Journal of Islamic Social Sciences 22 (1), 1-27, 2005 | 71 | 2005 |
| Chinese Muslims in colonial and postcolonial Indonesia M Ali Center for Southeast Asian Studies, University of Hawai'i at Manoa, 2007 | 37 | 2007 |
| The Muhammadiyah’s 47th Congress and “Islam Berkemajuan” M Ali Studia Islamika 22 (2), 377-386, 2015 | 31 | 2015 |
| Moderate Islam Movement in Contemporary Indonesia M Ali Islamic Thought and Movements in Contemporary Indonesia, 195-236, 2007 | 28 | 2007 |
| Fatwas on Inter-faith Marriage in Indonesia M Ali Studia Islamika 9 (3), 2022 | 27 | 2022 |
| Categorizing Muslims in Postcolonial Indonesia M Ali Moussons. Recherche en sciences humaines sur l’Asie du Sud-Est, 33-62, 2007 | 25 | 2007 |
| Islam and economic development in New Order's Indonesia (1967-1998) M Ali Honolulu: East-West Center, 2004 | 23 | 2004 |
| The concept of peace in the Qur’an: A socio-thematic analysis of Muslims’ contestation in Salatiga, Indonesia A Kuswaya, M Ali QIJIS (Qudus International Journal of Islamic Studies) 9 (1), 73-102, 2021 | 21 | 2021 |
| Transmission of Islamic knowledge in Kelantan M Ali Journal of the Malaysian Branch of the Royal Asiatic Society, 39-58, 2006 | 20 | 2006 |
| The internet, cyber-religion, and authority: the case of the Indonesian Liberal Islam Network M Ali Islam and Popular Culture in Indonesia and Malaysia, 101-122, 2011 | 17 | 2011 |
| Nationalism and Islam: perspective of Egyptian and Syrian Muslim intellectuals M Ali Indonesian Journal of Islam and Muslim Societies 4 (1), 51-79, 2014 | 16 | 2014 |
| ‘THEY ARE NOT ALL ALIKE’ Indonesian Muslim intellectuals' perception of Judaism and Jews M Ali Indonesia and the Malay World 38 (112), 329-347, 2010 | 13 | 2010 |
| Between faith and social relations: The muhammadiyah and nahdlatul ulama’s fatwas and ideas on non‐muslims and interreligious relations M Ali The Muslim World 110 (4), 458-480, 2020 | 12 | 2020 |
| Malaysia’s Islam Hadhari and the role of the nation-state in international relations M Ali Islam and International Relations: Contributions to Theory and Practice, 207-228, 2016 | 11 | 2016 |
| CONFRONTATION AND RECONCILIATION: Muslim Voices of Maluku Conflict (1999-2002) M Ali Journal of Indonesian Islam 1 (2), 379-402, 2023 | 9 | 2023 |
