AU Mic is a young planetary system with a resolved debris disc showing signs of planet formation and two transiting warm Neptunes near mean-motion resonances. Here we analyse three transits of AU Mic b observed with the CHaracterising ExOPlanet Satellite (CHEOPS), supplemented with sector 1 and 27 Transiting Exoplanet Survey Satellite (TESS) photometry, and the All-Sky Automated Survey from the ground. The refined orbital period of AU Mic b is 8.462995 ± 0.000003 d, whereas the stellar rotational period is P_rot = 4.8367 ± 0.0006 d. The two periods indicate a 7:4 spin–orbit commensurability at a precision of 0.1%. Therefore, all transits are observed in front of one of the four possible stellar central longitudes. This is strongly supported by the observation that the same complex star-spot pattern is seen in the second and third CHEOPS visits that were separated by four orbits (and seven stellar rotations). Using a bootstrap analysis we find that flares and star spots reduce the accuracy of transit parameters by up to 10% in the planet-to-star radius ratio and the accuracy on transit time by 3–4 min. Nevertheless, occulted stellar spot features independently confirm the presence of transit timing variations (TTVs) with an amplitude of at least 4 min. We find that the outer companion, AU Mic c, may cause the observed TTVs.