A new generation of cementitious materials is being engineered to selectively inhibit the growth of Acidithiobacillus, which are a key genera of acid-generating bacteria responsible for microbially induced concrete corrosion (MICC). In this context, the substitution of metal-laden granular activated carbon (GAC) particles and/or steel slag for a fraction of the fine aggregates traditionally used in concrete mixture has proven useful. While the antimicrobial properties of specific heavy metals (i.e. copper and cobalt) have been leveraged to inhibit acid-generating bacteria growth on sewer pipes, few studies have researched how biocidal aggregates may affect the microstructural and mechanical properties of cementitious materials. We report here on the effects that these biocidal aggregates substitutions can have on compressive strength, flowability, and setting times of cement-based formulations. Results showed that increases in compressive strength, regardless of the presence or absence of biocidal metals, resulted from the GAC incorporation where sand replacement was 3% by mass or lower, while flowability decreased when percentages higher than 3% of GAC was incorporated in a cement mix. When substituting fine aggregate with steel slag particles in mass ratios between 5% and 40%, compressive strength was not affected, regardless of the presence or absence of copper. Setting times were not affected by the inclusion of GAC or steel slag particles except when substituting GAC particles at 10% of the fine aggregate mass; under this condition both initial and final setting times were decreased. Results suggest that in order to have enhanced inhibition potential against acidophilic microorganisms and equal or improved mechanical properties, a combination of 1% metal-laden GAC and 40% copper-laden steel slag is an optimum fine aggregate substitution scenario.