Although the process of microbial degradation of coal to produce biomethane has got much attention from many research works, the products profiles of coal at the initial stage of methanogenic bioconversion are not clear yet. In this study, five coal-degrading bacterial strains (CD1, CD10, CD20, CD24, and CD25) from a methanogenic community were isolated and identified. Among them, CD1 and CD24 belong to Paenibacillus sp., CD10 and CD20 belong to Bacillus sp., and CD25 belongs to Stenotrophomonas sp. After biotreatment of lignite and bituminous coal, the kinds of newly produced compounds were 33 and 45, respectively. Metabolomics analysis showed that a large number of alkane compounds and heterocyclic aromatic compounds were produced after degradation of bituminous coal and lignite by isolated bacteria, and most of the compounds had been produced in a hydroxylated or acylated manner, indicating that the initial microbial treatment enhanced the bioavailability of coal. Some alkaloids and biosurfactants were also detected in the aforementioned products, such as glycerophosphocholine, proveratrol A, proveratrol B, surfactin, etc. These microbial metabolites may play an important role in solubilization during the degradation of coal. This study added to the understanding of the complicated metabolic process of methanogenic coal bioconversion and enabled effective production of biomethane with appropriate metabolic strategies. © 2021 The Authors. GCB Bioenergy published by John Wiley & Sons Ltd.