Successful implementation of bacteria-based self-healing in cracked cementitious materials requires the provision of a suitable incubation environment, which can activate the bacteria to produce e.g. calcium carbonate sealing the cracks. Research to date has focused on the self-healing process in humid air and water. However, almost all structures are built on or in the ground, thus, significant amounts of concrete are exposed to ground conditions. To investigate the effect of soil incubation on the self-healing process, laboratory experiments were conducted on mortar impregnated with Bacillus subtilis (encapsulated in calcium alginate). The mortar specimens were initially cracked and subdivided into three groups and each group was incubated for 28 days within different incubation environments, namely, partially-saturated soil, full-saturated soil, and water. Supported by Scanning Electron Microscope (SEM) and Energy Dispersive X-Ray Spectrometry (EDX), the results revealed that the bio self-healing can be activated within the cracks under the saturated regime of soil as far as the matric suction is smaller than the capillary pressure of the cracks. Moreover, the results indicated there was no evidence suggesting the influence of naturally existing bacteria in the soil on the self-healing process within the considered incubation period.