Antibiotic treatment failure of Staphylococcus aureus infections is very common. In addition to genetically encoded mechanisms of antibiotic resistance, numerous additional factors limit the efficacy of antibiotics in vivo. Identifying and removing the barriers to antibiotic efficacy is of major importance as even if new antibiotics become available, they will likely face the same barriers to efficacy as their predecessors. One major obstacle to antibiotic efficacy is the proficiency of S. aureus to enter a physiological state that is incompatible with antibiotic killing. Multiple pathways leading to antibiotic tolerance and the formation of tolerant sub-populations called persister cells, have been described for S. aureus. Additionally, S. aureus is a versatile pathogen that can infect numerous tissues and invade a variety of cell types, some of which are poorly penetrable to antibiotics. It is therefore unlikely that there will be a single solution to the problem of recalcitrant S. aureus infection. Instead, specific approaches may be required to target tolerant cells within different niches, be it through direct targeting of persister cells, sensitization of persisters to conventional antibiotics, improved penetration of antibiotics to particular niches or any combination thereof. Here we examine two well described reservoirs of antibiotic tolerant S. aureus, the biofilm and the macrophage, the barriers these environments present to antibiotic efficacy and potential solutions to the problem.