Self-assembled monolayers (SAMs) are promising materials for micromechanical applications. However, characterization of mechanical properties of monolayers is challenging for standard nanoindentation, and new efficient analysis techniques are needed. Hereby, a conventional nanoindentation method has been combined in a unique way with efficient data analysis based on consumed energy calculation and load-displacement data. The procedure has been applied on SAMs of 4, 4 ′ -biphenyldithiol (BPDT) on Au, 1-tetradecanethiol (TDT), and 1-hexadecanethiol (HDT) on Au and Ag substrates being the first study where SAMs of the same thiols on different substrates are analyzed by nanoindentation providing a new insight into the substrate effects. Unlike TDT and HDT SAMs, which are found to strongly enhance the homogeneity and stiffness of the underlying substrate, the BPDT covered Au substrate appears softer in mechanical response. In the case of TDT and HDT SAMs on Ag the structures are softer showing also faster relaxation than the corresponding structures on Au substrate. The proposed procedure enables a fast and efficient way of assessing the complex behaviour of SAM modified substrates. As a consequence, the results are relevant to practical issues dependent on layer activity and toughness.