Lipids are essential components of bacterial membranes and phages are quasi-ubiquitous in bacteria. In the human pathogen Staphylococcus aureus, two common prophages ϕ13 and ϕ11.1 are preferentially integrated in lipase genes, and act as regulatory switches of respectively Geh, a triglyceride lipase, and Hlb, a sphingomyelinase. The factors driving selection for this prophage conservation in lipase genes and the impact on S. aureus fitness are not well understood. We report that prophage status of both ϕ13 and ϕ11.1 affect membrane phospholipid composition and bacterial growth in serum. They vary the extent to which toxic C18:2, released from Geh activity on triglycerides, are incorporated in bacterial membranes. Hlb and Geh lipases lead respectively to palmitic acid C16 and linoleic acid C18:2, which compete for binding to fatty acid kinase subunit FakB1. When both lipases are active, interference from C16 decreases C18:2 incorporation via FakB1 and reduces fatty acid synthesis (FASII)-mediated elongation. In the presence of FASII inhibitor AFN-1252, S. aureus relies on exogenous fatty acids, and adapts faster when Hlb is intact (ϕ13 absent), but slower when Hlb is inhibited. Faster adaptation correlates with less incorporation of C18:2. These findings contribute to explaining the selective advantage of Hlb-conversion by ϕ13 as a means of increasing membrane plasticity and S. aureus adaptation to environmental lipids. They also reveal an effect of ϕ13 status on anti-FASII adaptation. Prophage status and host-specific lipid environments may be important for accurate prediction of S. aureus infection risk and efficacy of new therapeutics. Importance Staphylococcus aureus is a major cause of untreatable human bacterial infections and its lipases are crucial for virulence and immune response escape. Prophages inserted in these lipase-encoding genes able to reversibly switch their activities are common in S. aureus , but the selective benefits of their maintenance is little understood. We demonstrate that two prophages, inserted in triglyceride and sphingomyelin lipase genes, interactively modulate fatty acid incorporation into bacterial membranes. The presence or absence of these prophages determine how S. aureus adapts to lipid environments, by affecting membrane plasticity, bacterial fitness, and adaptation to an antibiotic inhibiting fatty acid synthesis. Our findings highlight the importance of assessing S. aureus prophages and host lipid environments when evaluating infection risk and therapy efficacy.