This work presents a combined experimental and simulation-based investigation of gas ow perturbations caused by atmospheric-pressure microwave plasma jet with modulated power. These plasma-induced ow instabilities are observed experimentally by schlieren imaging and the mechanism of their formation is explained using a numerical model. The model offers a time-resolved self-consistent solution of plasma dynamics, gas ow, and heat transfer equations. The simulation results are in good agreement with the experimental observations and we conclude that the key mechanism behind the ow perturbations is rapid gas heating at the end of the discharge tube.