In this paper we describe a systematic study comparing the properties of self-assembled monolayers (SAMs) formed by in situ deprotection and assembly of S-triphenylmethyl (trityl)- and thiolacetate-protected alkanethiols to those of SAMs formed from the parent alkanethiols. The two in situ deprotections were carried out in trifluoroacetic acid and THF/ammonium hydroxide, respectively. Monolayers of octadecanethiol (ODT) and the peptide-containing alkanethiol 3-mercapto-N-n-pentadecylpropionamide (1ATC15) were assembled on gold using the two in situ methods and characterized by contact angle goniometry, X-ray photoelectron spectroscopy, polarization modulation infrared reflection absorption spectroscopy, and electrochemical characterization methods to assess how the monolayer properties compare to those of monolayers prepared by traditional methods. The results for the in situ deprotection of the trityl-protected molecules demonstrate that this method can afford high-quality monolayers that are nearly indistinguishable from those prepared directly from alkanethiols. The quality of the monolayers prepared using this method is shown to depend on the solubility of the trityl-protected compound in trifluoroacetic acid. The results for the in situ deprotection of acetyl-ODT indicate this method yields low-quality monolayers that contain mixtures of adsorbates bound as thiolates and thiolacetates. In situ trityl deprotection is a useful approach for monolayer formation that greatly simplifies the purification, handling, and assembly of thiol-containing monolayer precursors.