The process of microbially induced carbonate precipitation (MICP) is known to effectively improve engineering properties of building materials and so does silk fibroin (SF). Thus, in this study, an attempt was taken to see the improvement in sand, that is, basic building material coupled with MICP and SF. Urease producing Bacillus megaterium was utilized for MICP in Nutri-Calci medium. To improve the strength of SF itself in bacterial solution, it was cross-linked with genipin at the optimized concentration of 3.12 mg/mL. The Fourier transform infrared (FTIR) spectra confirmed the crosslinking of SF with genipin in bacterial solution. In order to understand how such cross-linking can improve engineering properties, sand moulds of 50 mm3 dimension were prepared that resulted in 35% and 55% more compressive strength than the one prepared with bacterial solution with SF and bacterial solution only, respectively with higher calcite content in former one. The FTIR, SEM, x-ray powder diffraction spectrometry and x-ray photoelectron spectroscopy analyses confirmed higher biomineral precipitation in bacterial solution coupled with genipin cross-linked SF. As the process of MICP is proven to replace cement partially from concrete without negatively influence mechanical properties, SF cross-linked with genipin can provide additional significance in developing low-carbon cement-based composites.