Bacillus megaterium is a potential bioremediation and biocontrol agent. The accumulation of reserve polymers, such as poly-3-hydroxybutyrate (PHB), increases survival of B. megaterium in water. We used wild-type strains of this species and mutant strains deficient in PHB synthesis in soil microcosms for testing the hypothesis that differences in survival capabilities and spore quality between strains is maintained in heterogeneous environments enriched with organic matter. No differences in survival between strains, nor a decrease in bacterial cell numbers were observed in sterile soil microcosms. In non-sterile soil, the total cell number (vegetative cells plus spores) of the PHB wild-type strain was 3.5 times higher than that of the PHB-negative mutant. We suggest that for predictive purposes, validation of survival in a variety of conditions is necessary.