A comparative study of charge-transfer processes from/to methyl-terminated and carboxylate-terminated thiolate-covered Au(111) surfaces to/from immobilized methylene blue (MB) molecules is presented. Scanning tunneling microscopy images with molecular resolution reveal the presence of molecular-sized defects, missing rows, and crystalline domains with different tilts that turn the thickness of the alkanethiolate SAM (the spacer) uncertain. The degree of surface heterogeneity at the SAMs increases as the number of C units (n) in the hydrocarbon chain decreases from n = 6. Defective regions act as preferred paths for MB incorporation into the methyl-terminated SAMs, driven by hydrophobic forces. The presence of negative-charged terminal groups at the SAMs reduces the number of molecules that can be incorporated, immobilizing them at the outer plane of the monolayer. Only MB molecules incorporated into the SAMs close to the Au(111) surface (at a distance < 0.5 nm) are electrochemically active. MB molecules trapped in different defects explain the broad shape and humps observed in the voltammogram of the redox couple. The heterogeneous charge-transfer rate constants for MB immobilized into methyl-terminated thiolate SAMs are higher than those estimated for carboxylate- terminated SAMs, suggesting a different orientation of the immobilized molecule in the thiolate environment.