We tested the suitability of two spectroscopic methods, x-ray photoelectron spectroscopy (XPS) and time of flight secondary ion mass spectrometry (ToF-SIMS), in the recognition of bacterial and eukaryotic cell footprints on implant surfaces. Human mesenchymal stem cells (MSCs) and Staphylococcus aureus were cultured on sample surfaces and detached using trypsin. Scanning electron microscopy confirmed that the processed surfaces did not contain any human or microbial cells. The footprints were then analysed using XPS and ToF-SIMS. XPS results showed no significant differences between the footprints, but principal component analysis of the ToF-SIMS data enabled clear separation of MSC-footprints from the S. aureus and co-culture footprints (p < 0.03). ToF-SIMS also demonstrated ‘race for the surface’ between proteins, which suggest surface charge (zeta-potential) dependent protein adsorption. ToF-SIMS differentiated eukaryotic and bacterial footprints and has potential for post-hoc detection of implant-related infections based on the typical ToF-SIMS spectra.