Effective microorganism (EM) – a mixture of beneficial microbial formulation are extensively utilized worldwide in agriculture as plant growth promotor and biocontrol agent. Because of their wide spectrum usage, it is necessary to study the non‐target effect against the beneficial organisms used in crop production. Though, the wider applications of EM in agriculture and the environment have revealed, the environmental quality management of EM mainly metabolites‐ biochemical compounds derived from EM have yet to be studied. With this objective, the present study is undertaken to evaluate the compatibility of EM derived metabolites on the selected microbial biofertilizers, biocontrol agents including biopesticidal agents. Metabolites were extracted from the culture‐free broth of EM culture using various solvents and the extracted metabolites were characterized by the gas chromatography‐ mass spectroscopy (GC‐MS). The food poisoning technique was adapted for the screening of toxic effects. Toxic effect of the metabolites derived from the respective solvent was confirmed by measuring the growth of the respective microbial strain's vegetative growth and sporulation efficacy by dual plate assay, dual liquid assay, and spore germination microscopic slide assay. Active principles of the metabolites were readily extracted in all the solvents and the possible presence of bioactive metabolites were characterized by GC‐MS. There was no significant difference between the control and extract recorded. In the case of Rhizobium leguminosarum, the colony diameters of ethyl acetate and acetone extract were 1.6 and 1.8 cm, respectively, as in control (1.8 cm). Similar findings were also recorded for Azospirillum lipoferum, Phosphobacterium sp., and Pseudomonas flurescens. However, growth inhibition including spore germination was recorded in petroleum ether and acetone extract. Further study will be useful to exploit the principles of EM and EM derived metabolites in agriculture and environment without affecting non target beneficial organism.