A nitrogen-starving isolation strategy was developed for the first time to screen bacteria with high calcium-precipitating activity (CPA) for bioremediation of damage in porous media. Meanwhile, a novel mini-tube method based on the detection of insoluble Ca was established to evaluate the CPA of the isolates. A low-nitrogen-demanding strain B6, identified as Bacillus sp., was screened to exhibit the highest CPA (55 mM insoluble Ca). Furthermore, the effects of environmental factors and nutrient availability on B6-induced calcium precipitation were evaluated. The results show that nitrate and starch are the best nitrogen source and carbon source with optimal concentration being 4 and 2 g L, respectively. The suitable pH range for B6 to precipitate calcium is from 8.5 to 10.5. B6 can maintain the highest CPA at an initial spore concentration of 1.0 × 10 spores·mL. The optimal CaO dosage is 10 g L. Finally, the calcite precipitation is confirmed by ESEM, EDS, and XRD analysis.