Abstract: Since its diffusion in the 17th century, corpuscular philosophy appeared to Catholic circles as a mortal danger for creation, providence, free will and, in particular, the philosophical foundations of the doctrine of the transubstantiation of the Eucharist. This contribution traces and analyzes the debate concerning the complex relationship between atomism and atheism in the last decades of the seventeenth century in Naples, especially during the trial against the so-called atheists (1688-1697).