Sub-standard soils are of great concern worldwide due to diverse economic losses and the possibility of severe environmental hazards ranging from catastrophic landslides, building collapse, and erosion to loss of lives and properties. This study explored the potential of urease-producing bacteria, Bacillus cereus and Bacillus paramycoides, to stabilise sub-standard soil bio-stabilisation. The maximum urease activity measured by B. cereus and B. paramycoides was 665 U/mL and 620 U/mL, respectively. B. cereus and B. paramycoides precipitated 943 ± 57 mg/L and 793 ± 51 mg/L of CaCO3 at an optical density (425 nm) of 1.01 and 1.09 and pH 8.83 and 8.59, respectively, after 96 hours of incubation. SEM microstructural analysis of the precipitated CaCO3 revealed crystals of various sizes (2.0–23.0 µm) with different morphologies. XRD analysis confirmed that the precipitated CaCO3 comprised calcite and aragonite crystals. SEM analysis of the microstructure of organic and sandy clay soils treated with B. cereus and B. paramycoides showed the formation of bio-precipitated calcium carbonate deposits on the soil particles (biocementing soil grains), with B. cereus precipitating more CaCO3 crystals with a better biocementing effect compared to B. paramycoides. Overall, the experimental results attributed CaCO3 formation to bacterial-associated processes, suggesting that soil ureolytic bacteria are potentially useful to stabilise sub-standard soil.