The catalytic activity of two common bacterial enzymes, lactate dehydrogenase (LDH) and cytochrome c oxidase (COX) from Escherichia coli, was examined following bacterial exposure to microwave (MW) radiation under well-defined experimental conditions. The experiments were conducted in a specialised microwave processing apparatus, with an exposure frequency of 18 GHz, and a temperature profile that was restricted to below 40oC to avoid thermal degradation of the bacteria. The absorbed power was calculated to be 1500 kW/m3 and the electric field was determined to be 300 V/m. Both values were theoretically confirmed using Computer Simulation Technology (CST) Microwave Studio 3D Electromagnetic Stimulation Software. Results showed that the activity of both enzymes was increased following MW radiation compared to negative controls and thermally treated samples subjected to similar temperature profiles. It is suggested that the increase in COX and LDH enzyme activity could not be explained by conventional heating alone, but was rather a result of micro-thermal effects that incorporated ‘undetectable’ thermal mechanisms.