In this work, a novel synthesis of homogeneous molybdenum silicate spheres under non-aqueous conditions is presented. A preparation method is based on the condensation of molybdenum metal–organic framework-based precursor solution prepared via a microwave-assisted approach from bis(acetylacetonato)dioxomolybdenum and biphenyl-4,4′-dicarboxylic acid with 3-aminopropyltriethoxysilane under non-aqueous conditions. The as-prepared product was calcined at 500 °C to obtain amorphous and porous molybdenum silicate microspheres with homogeneously distributed molybdenum species within silicate matrix. The microspheres exhibit an average size of about 480 nm. This material was further studied as a heterogeneous catalyst for the epoxidation of olefins via the model catalytic epoxidation of cyclohexene with cumylhydroperoxide. High catalytic activity at the moderate temperature (65 °C) with the conversion of 86% after 2 h and the high selectivity to cyclohexene oxide has been achieved. In addition, molybdenum silicate microspheres exhibit catalytic activity and high selectivity in the oxidation of aniline to nitrosobenzene.