This study investigated the potential of agro-waste-derived substrates to support fungal-mediated biomineralization of calcium carbonate for the production of calcite-rich biocomposites with potential cementitious applications. Rice bran powder and eggshell powder were evaluated as organic nutrient and calcium sources, respectively, to support the growth of Penicillium sp. isolated from environmental soil samples. Five experimental treatments were monitored over a 28-day incubation period and characterized using XRD, XRF, and FTIR. The integrated system (T5) exhibited an initial decrease in pH to 5.89, followed by pH recovery to 8.14 by Day 28, indicating changes in the chemical environment during incubation that were favorable for calcium carbonate precipitation. T5 exhibited a 21.53% reduction in solid-phase mass during incubation. Quantitative Rietveld analysis indicated that calcite accounted for 100% of the quantified crystalline phase assemblage in T5, with no detectable aragonite or vaterite within the resolution and detection limits of the analysis. The Rietveld refinement yielded an Rwp of 9.14%, indicating reasonable agreement between the experimental and calculated diffraction profiles. XRF analysis showed a high CaO content (46.04%) together with silica and potassium in the resulting material. FTIR spectroscopy identified organic functional groups and carbonate-associated vibrational bands, providing complementary evidence for the organic and inorganic components of the product. These findings indicate that rice bran and eggshell wastes can serve as alternative organic nutrient and calcium sources, respectively, for Penicillium sp. to produce calcite-rich material for sustainable cementitious applications.