Fluorescent gold nanoclusters (AuNCs) with an average diameter of 2.7 ± 1.0 nm stabilized with 11-mercaptoundecanoic acid were supported on halloysite nanotubes modified with aminosilane. The cytotoxicity of the obtained fluorescent material was investigated in A549 human cells. The AuNCs stabilized on halloysite showed good uptake by the cells. The material did not cause a pronounced toxic effect and visible membrane damage within the 25–50 μg/mL concentration range. An increase in nanocomposite concentration to 100 μg/mL led to massive cell death via apoptosis. This concentration-dependent toxicity mechanism allows for using AuNCs stabilized on halloysite for halloysite visualization in biological objects, bioimaging, and cancer therapy