Treatment of methicillin-resistant Staphylococcus aureus (MRSA) infections is challenging and is associated with high rates of therapeutic failure. The glycopeptide (GP) vancomycin and the lipopeptide (LP) daptomycin are still relied upon to manage invasive MRSA infections; however, resistance to these antibiotics has emerged and there is evidence of cross-resistance between them. It has been observed that the susceptibility of MRSA to beta-lactams increases as susceptibility to GPs and LPs decreases, a phenomenon termed the seesaw effect. Recent efforts to understand the mechanism underlying the seesaw effect have focused on the penicillin binding proteins (PBPs). However, while daptomycin resistance is largely mediated by remodeling of membrane lipid composition, the role of membrane lipids in producing cross-resistance and the seesaw effect has not yet been investigated. Here, we evaluate the lipid profiles, cross susceptibilities, and beta-lactam susceptibilities of a collection of isogenic MRSA strains selected against daptomycin, vancomycin or dalbavancin (a lipoglycopeptide; LGP) to assess the relationship between membrane composition, cross-resistance, and the seesaw effect. We found that modification of membrane composition occurs not only in daptomycin-selected strains, but also vancomycin- and dalbavancin-selected strains. Significantly, we observed that typically the levels of short-chain phosphatidylglycerols (PGs) negatively correlate with MICs of GP/LP/LGP and positively correlate with MIC of certain beta-lactams, the latter being dependent on the primary PBP target of the particular beta-lactam. Furthermore, changes to certain PGs with long-chain fatty acids correlate well with presence of the seesaw effect. These studies demonstrate a major association between membrane remodeling and the seesaw effect.