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Rice is a popular food in Africa, but current yield achieved is far lower than the yield potential due to abiotic/biotic stresses. We recently demonstrated that commercially formulated products of Bacillus subtilis and Trichoderma asperellum strains increased rice yield when applied as transplant dipping or post-transplanting foliar sprays in Tanzania (Africa). Further experiments were conducted to investigate: (1) synergies in alternate use of B. subtilis and T. asperellum products as dipping or foliar spray in Tanzania, and (2) effects of coating seeds with Serratia nematodiphila in Kenya (Africa). In Tanzania, using formulated B. subtilis and T. asperellum products led to > 100% increase in yield. Furthermore, alternative use of B. subtilis and T. asperellum as transplant dipping or post-transplanting foliar spray led to further yield increase (ca. 32%) over the use of single-organism products at both times. Microbial treatments led to significant reductions in rice blast. In comparison with the fungicide treatment, increased yield with using microbial products appeared to have resulted mostly from improved plant development rather than reduced rice blast per se. At the Kenyan site where current yield is relatively high, the overall yield increase associated with microbial products was limited although statistically significant. Coating seeds with one specific S. nematodiphila strain led to grain yield comparable to applying microbial products as transplant dipping and post-transplanting foliar spray. The present study suggests that the formulated microbial products can significantly improve rice productivity in subsistence farming and should be applied in alternation over time to exploit their synergies.