Context. Stellar flares of active M dwarfs can affect the atmospheric composition of close-orbiting gas giants, and can result in time-dependent transmission spectra. Aims. We aim to examine the impact of a variety of flares, differing in energy, duration, and occurrence frequency, on the composition and transmission spectra of close-orbiting, tidally locked gaseous planets with climates dominated by equatorial superrotation. Methods. We used a series of pseudo-2D photo- and thermochemical kinetics models, which take advection by the equatorial jet stream into account, to simulate the neutral molecular composition of a gaseous planet ( T eff = 800 K) that orbits a M dwarf during artificially constructed flare events. We then computed transmission spectra for the evening and morning limb. Results. We find that the upper regions (i.e. below 10 μbar) of the dayside and evening limb are heavily depleted in CH 4 and NH 3 up to several days after a flare event with a total radiative energy of 2 × 10 33 erg. Molar fractions of C 2 H 2 and HCN are enhanced up to a factor three on the nightside and morning limb after day-to-nightside advection of photodissociated CH 4 and NH 3 . Methane depletion reduces transit depths by 100–300 parts per million (ppm) on the evening limb and C 2 H 2 production increases the 14 μm feature up to 350 ppm on the morning limb. We find that repeated flaring drives the atmosphere to a composition that differs from its pre-flare distribution and that this translates to a permanent modification of the transmission spectrum. Conclusions. We show that single high-energy flares can affect the atmospheres of close-orbiting gas giants up to several days after the flare event, during which their transmission spectra are altered by several hundred ppm. Repeated flaring has important implications for future retrieval analyses of exoplanets around active stars, as the atmospheric composition and resulting spectral signatures substantially differ from models that do not include flaring.