The microbial precipitation of CaCO3 is an emerging strategy for the consolidation of decayed limestone. Strains of Bacillus sp. and Micrococcus sp. isolated from black crusts were selected by polycyclic aromatic hydrocarbon enrichment culture and tested for their ability to precipitate CaCO3 by induced mineralization. Among the isolates, Bacillus sp. A2, B1, B5 and Micrococcus sp. A10 produced the largest quantities of biogenic calcite. Stone bio-consolidation was then tested using Carbogel as a carrier. The most efficient bio-cementation on limestone slabs was achieved by Bacillus sp. A2 and B1 and Micrococcus sp. A10. Bio-consolidation treatments were also applied to fragmented stones from the Church of Santa Maria dei Miracoli by inoculating the three bacterial strains individually or as a mixture. Bacillus sp. A2, Micrococcus sp. A10 and the mixture achieved the most efficient consolidation. Our data showed that Carbogel provides an appropriate substitute for natural biofilm formation in bio-consolidation protocols. Scanning electron microscopy and energy-dispersive X-ray spectroscopy revealed calcified bacterial cells filling the pores of stone specimens, increasing the calcium content by 100% more than a non-inoculated control treatment under the same conditions. Our new bio-consolidation protocol therefore provides an effective strategy to prevent the further deterioration of stone monuments. Display omitted •PAH-acclimated Bacillus sp. and Micrococcus sp. can precipitate calcite.•Calcite formation involves an induced mineralization mechanism.•Biofilm formation can contribute to the bio-consolidation process.•Carbogel can substitute for biofilm formation in bio-consolidation protocols.•Carbogel is therefore a suitable carrier for bio-consolidation applications.