The oxides of the transition metal molybdenum exhibit excellent antimicrobial properties. We present the preparation of molybdenum trioxide dihydrate (MoO3×2H2O) by an acidification method and demonstrate the thermal phase development and morphological evolution during and after calcination from 25 °C to 600 °C. The thermal dehydration of the material was found to proceed in two steps. Microbiological roll-on tests using Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa were performed and exceptional antimicrobial activities were determined for anhydrous samples with orthorhombic lattice symmetry and a large specific surface area. The increase in the specific surface area is due to crack formation and to the loss of the hydrate water after calcination at 300 °C. The results support the proposed antimicrobial mechanism for transition metal oxides, which based on a local acidity increase as a consequence of the augmented specific surface area.