Porphyromonas gingivalis is the keystone pathogen associated with chronic periodontitis. The bacterium’s main virulence factors are its cell surface-located cysteine proteases, the Arg-gingipains (RgpA, RgpB) and the Lys-gingipain (Kgp). These proteinases are synthesized as inactive precursors with propeptides that inhibit proteinase function thus preventing premature activation. The long-term goal to design propeptides with enhanced affinities and improved resistance to proteolysis, capable of sustained inhibition against mature cognate gingipains. The aim of this study was to characterize the inhibitory potential of the Kgp and RgpB propeptides against the mature cognate enzymes. Recombinant propeptides of Kgp, RgpB, and RgpA with N-terminal His-tags were produced in Escherichia coli. The inhibition was examined within assays measuring proteolytic activity observed from whole cells and purified proteases. The propeptides from Kgp and RgpB demonstrated strong selectivity for their cognate proteases. However the inhibitory potential of the rKgp propeptide was low. The rKgp propeptide demonstrated a propensity to aggregate and in particular form homodimers including homodimers stabilized by a disulphide bridge. The rKgp propeptide with the residue Cys16 was changed to Ser16 by site directed mutagenesis. Although freezing-induced precipitation was observed, this mutated propeptide did not form homodimers. In conclusion using site-directed mutagenesis to alter residues is a promising strategy in the development of a gingipain propeptides-based therapeutic for the treatment of periodontitis.