Staphylococcus aureus biofilms are tolerant to antibiotics and disinfectants. Staphylococci cell walls, principally composed of peptidoglycan, are a key target for antimicrobial agents. S. aureus proteomics and cell walls, grown as planktonic organisms, 3-day hydrated biofilm, 12-day hydrated biofilm and 12-day dry surface biofilm (DSB) were analysed. High-throughput tandem mass tag-based mass spectrometry showed upregulation of proteins involved in cell wall synthesis in biofilms compared to planktonic growth. Bacterial cell wall width (measured by transmission electron microscopy) and peptidoglycan production (detected using a silkworm larva plasma system) increased with biofilm culture duration (P < 0.001) and dehydration (P = 0.002). Similarly, disinfectant tolerance was greatest in DSB, followed by 12-day hydrated biofilm, then 3-day biofilm and least in planktonic bacteria, suggesting cell wall is one of the key determinants for S. aureus biofilm biocide resistance. Our findings shed light on possible new target to combat biofilm-related infections and hospital dry surface biofilms.