Little is known about the background of atheism in Malaysia and how Muslims respond to the phenomenon, although provocations by Malaysian atheists often take place on social media. This study addressed the gap by exploring the atheism phenomenon in Malaysia’s ethnoreligious-oriented society. Data were collected from in-depth interviews and content analysis using the qualitative method. All data were analysed thematically using the software for qualitative analysis, ATLAS.ti. The resulting superordinate themes that emerged from the analysis include the phenomenon of Malaysian (...) atheism, the factors for becoming atheists and the theme of arguments. The study’s findings are three-fold. Firstly, atheism started in Malaysia after globalisation began. Secondly, most Malaysian atheists were influenced by internal factors based on emotional–psychological elements rather than being scientifically oriented. Last but not least, the main themes of Malaysian atheist arguments are ‘God’s justice’, ‘the problem of evil’ and ‘science rationalism’. As a response, Muslims counter the atheism phenomenon by providing an effective approach to preserving social cohesion and harmony in an ethnoreligious society.Contribution: This article suggests that although atheism is regarded as a challenge to society since Malaysia is an ethnoreligious-oriented society, atheism needs to be countered through proper education as early prevention, besides encouraging healthy discussions. (shrink)