Abstract Since the 1990s, Indonesia has been confronted with the growing influence of a radical Islamist movement that challenges the state doctrine (Pancasila), which was adopted in 1945, and demands a greater place for Islam, which is the religion of nearly 90 per cent of the population. The hardline groups wish to call into question the Indonesian state’s pluralistic and inclusive religious identity, which they see as a conspiracy hatched by the Christian minority to deprive the Muslim majority of its ostensible rights. The Society of Jesus, which has been present in Java since the nineteenth century, is considered by Islamist critics as the main architect of this alleged plot. Furthermore, one of its members, Father Josephus Beek, is presented by Islamist radicals as one of the founders of the New Order (1966–1998), the regime led by General Suharto which was very hostile to political Islam in its early days. This article analyses how the Society of Jesus was able to integrate Catholicism into the Javanese spiritual landscape and explores the subsequent roles played by Jesuit leaders in the genesis and defence of Pancasila. It also sheds light on how Josephus Beek’s very real manoeuvres have provided fodder for militant Islamist circles seeking to delegitimate Indonesia’s secular status quo.