Recently it has been shown that psychiatric disorders are associated with changes in the host microbiome. Little is known about the association of electroconvulsive therapy (ECT) and microbiome alterations. In our pilot-study, 15 patients with severe or treatment resistant depression were prospectively recruited and oral swabs were collected pre- and post-ECT. Compared to a control group, ECT did not lead to a significant microbial shift in longitudinal samples (p = 0.65). However, alpha diversity measurements significantly differed between responders and non-responders before ECT (observed species p = 0.014, Shannon p = 0.03) and after ECT (observed species p = 0.015, Shannon p = 0.13).