Streptococcus pyogenes (group A Streptococcus-GAS) is an important pathogen for humans. GAS has been associated with severe and invasive diseases. Despite the fact that these bacteria remain universally susceptible to penicillin, therapeutic failures have been reported in some GAS infections. Many hypotheses have been proposed to explain these antibiotic-unresponsive infections, however none of them have fully elucidated this phenomenon. In this study, we show that GAS strains have the ability to form antimicrobial-persistent cells when growing on abiotic surfaces in a biofilm-like environment. Our data suggest that efflux activity was possibly involved in this phenomenon. In fact, gene expression assays by real-time qRT-PCR showed upregulation of some genes associated with efflux pumps in persistent cells arising in the presence of penicillin. Phenotypic reversion assay and whole-genome sequence analysis indicated that this event was due to non-inherited resistance mechanisms. The small persistent colonies showed downregulation of genes associated with protein biosynthesis and cell growth, as demonstrated by gene expression assays. Moreover, the proteomic analysis showed that susceptible cells express higher levels of ribosome proteins. It is conceivable to suppose that the generation of persistent cells by S. pyogenes might a mechanism of antimicrobial refractory during the course of real GAS invasive infections, which has been overlooked. Accordingly, the phenomenon described here might shed some light on the origin of therapeutic failures in S. pyogenes infections. Multifactorial mechanisms involving efflux pump activity, protein synthesis inhibition and cell-growth impairment seem to play roles in generation of GAS-persistent cells.