Global warming profoundly impacts the functioning of aquatic ecosystems. Nonetheless, the effect of warming on primary producers is poorly understood, especially periphyton production, which is affected both directly and indirectly by temperature-sensitive top-down and bottom-up controls. Here, we study the impact of warming on gross primary production in experimental ecosystems with near-realistic foodwebs during spring and early summer. We used indoor mesocosms following a temperate temperature regime (control) and a warmed (+4 °C) treatment to measure biomass and production of phytoplankton and periphyton. The mesocosms’ primary production was dominated by periphyton (>82%) during the studied period (April-June). Until May, periphyton production and biomass were significantly higher in the warm treatment (up to 98% greater biomass compared to the control) due to direct temperature effects on growth and indirect effects resulting from higher sediment phosphorus release. Subsequently, enhanced grazer abundances seem to have counteracted the positive temperature effect causing a decline in periphyton biomass and production in June. We thus show, within our studied period, seasonally distinct effects of warming on periphyton, which can significantly affect overall ecosystem primary production and functioning.