The provision of suitable incubation environments is vital for successful implementation of bio self-healing concrete (bio-concrete). We investigated the effect of soil incubation to examine if the self-healing process can be activated in comparison with the conventional incubation environment (water). The data was collected from laboratory-scale experiments conducted on mortar specimens. The mortar was impregnated with Bacillus subtilis and this bacteria was encapsulated in calcium alginate for protection from the production process. The mortar specimens were mechanically cracked and then incubated within fine-grained fully saturated natural soil for about 4 weeks. The cracks were inspected before and after incubation by light microscopy to evaluate the healing ratio. The mineral precipitations on crack surfaces were examined by Scanning Electron Microscope (SEM) and Energy Dispersive X-Ray Spectrometry (EDX). The data reflects the efficiency of bio-concrete for certain structures such as tunnels and deep foundation, where concrete elements are exposed to ground conditions.