An in-depth mechanistic understanding of the interaction between stainless steel surfaces and proteins is essential from a corrosion and protein-induced metal release perspective when stainless steel is used in surgical implants and in food applications. The interaction between lysozyme (LSZ) from chicken egg white and bovine serum albumin (BSA) and AISI 316L stainless steel surfaces was studied ex situ by means of X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) after different adsorption time periods (0.5, 24, and 168 h). The effect of XPS measurements, storage (aging), sodium dodecyl sulfate (SDS), and elevated temperature (up to 200 °C) on the protein layers, as well as changes in surface oxide composition, were investigated. Both BSA and LSZ adsorption induced an enrichment of chromium in the oxide layer. BSA induced significant changes to the entire oxide, while LSZ only induced a depletion of iron at the utmost layer. SDS was not able to remove preadsorbed proteins completely, despite its high concentration and relatively long treatment time (up to 36.5 h), but induced partial denaturation of the protein coatings. High-temperature treatment (200 °C) and XPS exposure (X-ray irradiation and/or photoelectron emission) induced significant denaturation of both proteins. The heating treatment up to 200 °C removed some proteins, far from all. Amino acid fragment intensities determined from ToF-SIMS are discussed in terms of significant differences with adsorption time, between the proteins, and between freshly adsorbed and aged samples. Stainless steel-protein interactions were shown to be strong and protein-dependent. The findings assist in the understanding of previous studies of metal release and surface changes upon exposure to similar protein solutions.