In this work, CoFe2O4 nanoparticles were prepared successfully under microwave irradiation (MW-CoFe2O4) using a heterometallic oxo-centered trinuclear [CoFe2O(CH3COO)6(H2O)3]2H2O complex as precursor and compared with conventional thermal method (CT-CoFe2O4). The nanoparticles of MWCoFe2O4 and CT-CoFe2O4 were characterized by physicochemical methods. The X-ray diffraction results revealed that both MW-CoFe2O4 and CT-CoFe2O4 nanoparticles adopt a cubic spinel structure. The SEM images of MW-CoFe2O4 and CT-CoFe2O4 show flower-like morphology with average diameter size 9 and 33 nm, respectively. The MW-CoFe2O4 as a sonocatalyst was used for degradation of methylene blue and Rhodamine-B with conversion percent of 98% and 90%, respectively, which is up to fifty percent more than what recorded for CT-CoFe2O4 activity. The higher catalytic activity of MW-CoFe2O4 is related to its smaller particle size and higher porosity compared to CT-CoFe2O4 nanoparticles. These magnetic sonocatalysts were easily separated from reaction mixture by a magnet and reused without significant loss of activity. Also, a plausible mechanism through hydroxyl radical path was postulated.