A 3D stack-of-stars MR-thermometry sequence was developed and evaluated during hepatic microwave ablation in a chicken phantom. A commercially available microwave generator (MWG) working in pulsed mode controlled by a temperature sensor was used. Results show a spatially dependent phase-offset in the MR-image only during active ablation mode of the pulsed MWG impairing thermometry. Consequently, 73% of thermometry data were discarded for the fixed phantom yielding a temperature precision of 0.72°C±0.60°C whereas 94% were discarded for the moving phantom with an accuracy of 1.08°C±1.25°C. For clinical MR-thermometry, an MWG with less EMI is required to improve resolution and temperature precision.