Self-assembled monolayers (SAMs) of alkanethiolates on gold are chemically defined substrates that can be used to evaluate the effects of an immobilized biomolecule. However, the types of biomolecules that can influence stem cell behavior are numerous and inter-related, and efficient experimental formats are a critical need. Here we employed a SAM array technology to investigate the effects of multiple, distinct peptides and peptide combinations on human mesenchymal stem cell (hMSC) behavior. Specifically, we characterized the conjugation of peptide mixtures to SAM arrays and then investigated the combined effects of a bone morphogenic protein receptor-binding peptide (BR-BP), a heparin proteoglycan-binding peptide (HPG-BP), and varied densities of the integrin-binding ligand Gly-Arg-Gly-Asp-Ser-Pro (GRGDSP) on hMSC surface coverage and alkaline phosphatase activity. Results indicate that an amine reactive fluorescent probe can be used to characterize peptide composition after immobilization in SAM array spots. Furthermore, hMSC response to BR-BP and HPG-BP is dependent on GRGDSP density and at day 7, hMSC alkaline phosphatase expression is highly dependent on GRGDSP density. Taken together, we demonstrate how a SAM array approach can be used to probe the combinatorial effects of multiple peptides and motivate further investigations into potential synergies between cell adhesion and other bioactive peptides.