Bioglycerol must be valorized to make biodiesel competitive vis-à-vis petro-diesel price. Glycerol carbonate is a sustainable chemical used by many industries. Various routes are reported but there exists a scope to develop better catalytic routes for selective synthesis of glycerol carbonate. Different polymorphs of MnO2 were explored as catalyst for the first time in the synthesis of glycerol carbonate by transesterification of glycerol with dimethyl carbonate under solvent-free conditions. The effect of microwave condition versus conventional heating was compared vis-a-vis conversion of glycerol, selectivity of glycerol carbonate and glycidol. Microwave heating (80 °C) was advantageous over conventional heating (120 °C). Different mesoporous polymorphs of MnO2 were prepared by hydrothermal synthesis and the activity of each polymorph was screened for transesterification reaction of glycerol. All MnO2 polymorphs were completely characterized. δ-MnO2 was the most active, selective, robust and recyclable catalyst. A kinetic model was developed. The overall process is green and sustainable.