Abstract Study Objectives Microstates are semi-stable voltage topographies that account for most of electroencephalogram (EEG) variance. However, the impact of time of the day and sleep on microstates has not been examined. To address this gap, we assessed whether microstates differed between the evening and morning and whether sleep slow waves correlated with microstate changes in healthy participants. Methods Forty-five healthy participants were recruited. Each participant underwent 6 minutes of resting state EEG recordings in the evening and morning, interleaved by sleep EEGs. Evening-to-morning changes in microstate duration, coverage, and occurrence were assessed. Furthermore, correlation between microstate changes and sleep slow-wave activity (SWA) and slow-wave density (SWD) were performed. Results Two-way ANOVAs with microstate class (A, B, C, and D) and time (evening and morning) revealed significant microstate class × time interaction for duration (F(44) = 5.571, p = 0.002), coverage (F(44) = 6.833, p = 0.001), and occurrence (F(44) = 5.715, p = 0.002). Post hoc comparisons showed significant effects for microstate C duration (padj = 0.048, Cohen’s d = −0.389), coverage (padj = 0.002, Cohen’s d = −0.580), and occurrence (padj = 0.002, Cohen’s d = -0.606). Topographic analyses revealed inverse correlations between SWD, but not SWA, and evening-to-morning changes in microstate C duration (r = −0.51, padj = 0.002), coverage (r = −0.45, padj = 0.006), and occurrence (r = −0.38, padj = 0.033). Conclusions Microstate characteristics showed significant evening-to-morning changes associated with, and possibly regulated by, sleep slow waves. These findings suggest that future microstate studies should control for time of day and sleep effects.