Staphylococcus aureus is a major human pathogen responsible for severe infections. While traditionally described as extracellular, increasing evidence establishes S. aureus as a facultative intracellular pathogen. Intracellularity contributes to immune evasion, dissemination, and antibiotic failure. To identify bacterial factors critical for S. aureus invasion, intracellular replication, persistence, and host cytotoxicity, we screened a comprehensive collection of 1,920 S. aureus mutants (Nebraska transposon mutant library) in epithelial cells across five timepoints (0.5 to 48 hours post-infection). We identified 73 bacterial factors strongly modulating S. aureus intracellularity, including mutants displaying multiple phenotypes. Most of these factors have not been linked to intracellular lifestyle. Among these, we characterized the nicotinamidase PncA as a novel regulator of the agr system via redox state modulation, strongly impacting virulence. This study provides a systematic analysis of S. aureus factors critical for intracellular lifestyle, with implications for the development of antimicrobial strategies targeting this resilient bacterial population.