Use of microbial biofertilizers, biocontrol agents and biopesticides is in the rise in developing countries like India. Most of the microbial inoculants are isolated from a given soil agro-climatic zone and are mass multiplied and used in agricultural fields all over the country. Inconsistency in the field performance of microbial inoculants can be attributed to issues like adaptability to a non-native soil, negative effects of interaction with existing microbes in crop environment and incompatibility in colonizing different crop hosts, species and varieties. Every crop plant is known to be evolved with its compatible microbiome and hence the introduction of new microbes might have a definitive impact on the microbial balance in the soil and crop environment. Understanding of the microbe-microbe interaction alongside with development of crop specific microbiome blueprints is emphasised. Microbial testing of soil is recommended before cropping season for a more optimized use of biofertilizers and biocontrol agents for an enhanced field performance of microbial inoculants and better crop yields. © 2017 Elsevier B.V.