As a result of global climate change the incidence of drought conditions in Europe is predicted to increase in the future, which also influences plant resistance. Lipids are important plant constituents that protect plants against drought stress and contribute to the intermediate stable carbon (C) pool in soil. However, the extent to which drought influences lipid cycling in the plant–soil system is unknown and, therefore, it remains questionable how the ecosystem recovers after drought. We focused on plant and soil samples from two different plant communities (temperate grassland and heathland) that had been exposed to 5 years of 4.5–6.0 weeks repeated annual drought. They were sampled one year after the last drought to check the recovery of the plant–soil system. Samples were analyzed for their bulk C, stable C and nitrogen (N) isotope (δ¹³C, δ¹⁵N) and lipid composition. Contrary to our expectation, no strong influence of five years of repeated annual drought was observed for above-ground biomass, roots and soils in the model ecosystems with respect to elemental (C and N concentrations, C : N ratio) bulk isotope (δ¹³C, δ¹⁵N) composition and the total extractable lipid concentration. Thus, plants did not sustain a significant change in their C and lipid concentration as well as their composition after five years of repeated annual drought. This might be related to the comparatively short drought period related to the overall growth season and provides evidence for recovery of the C and lipid dynamics in temperate grassland and heathland model ecosystems exposed to annual drought.