Although estuarine microphytobenthos (MPB) is frequently exposed to excessive light and temperature conditions, little is known on their interactive effects on MPB primary productivity. Laboratory and in situ experiments were combined to investigate the short‐term joint effects of high light (HL) and high temperature (37°C versus 27°C) on the operating efficiency of photoprotective processes [vertical migration versus non‐photochemical quenching (NPQ)] exhibited by natural benthic diatom communities from two intertidal flats in France (FR) and Portugal (PT). A clear latitudinal pattern was observed, with PT biofilms being more resistant to HL stress, regardless the effect of temperature, and displaying a lower relative contribution of vertical migration to photoprotection and a stronger NPQ in situ. However, higher temperature leads to comparable effects, with photoinhibition increasing to about three times (i.e. from 3% to 10% and from 8% to 22% in PT and FR sites respectively). By using a number of methodological novelties in MPB research (lipid peroxidation quantification, Lhcx proteins immunodetection), this study brings a physiological basis to the previously reported depression of MPB photosynthetic productivity in summer. They emphasize the joint role of temperature and light in limiting, at least transiently (i.e. during emersion), MPB photosynthetic activity in situ.