Most studies assessing the combined effects of chemical and non-chemical stressors on aquatic ecosystems have been based on synchronous stressor applications. However, asynchronous exposure scenarios may be more common in nature, particularly for pulsed stressors such as heatwaves and pesticide concentration peaks. In this study, we investigated the single and combined effects of the insecticide chlorpyrifos (CPF) and a heatwave (HW) on a zooplankton community representative of a Mediterranean coastal wetland using synchronous (CPF+HW) and asynchronous (HW→CPF and CPF→HW) exposure scenarios. CPF was applied at a concentration of 0.8 µg/L (single pulse), and the HW was simulated by a temperature increase of 8°C above the control temperature (20°C) for 7 days in freshwater microcosms. The interaction between stressors in synchrony resulted in synergistic effects at the population level (Daphnia magna) and additive at the community level. The partial reduction of sensitive species resulted in an abundance increase of competing species that were more tolerant to the evaluated stressors (e.g. Moina sp.). The asynchronous exposure scenarios resulted in a similar abundance decline of sensitive populations as compared to the synchronous one; however, the timing of stressor resulted in different responses in the long term. In the HW→CPF treatment, the D. magna population recovered at least one month faster than in the CPF+HW treatment, probably due to survival selection and cross-tolerance mechanisms. In the CPF→HW treatment, the effects lasted longer than in the CPF+HW, and the population did not recover within the experimental period, most likely due to the energetic costs of detoxification and effects on internal damage recovery. The different timing and magnitude of indirect effects among the tested asynchronous scenarios resulted in more severe effects on the structure of the zooplankton community in the CPF→HW treatment. Our study highlights the relevance of considering the order of stressors to predict the long-term effects of chemicals and heatwaves both at the population and community levels. Display omitted •Chlorpyrifos and heatwaves can produce synergistic effects on zooplankton species.•The order of stressors affects the long-term response of sensitive species.•Effects of the stressor sequence are propagated at the community level.•Chlorpyrifos followed by heatwaves produce the most harmful effects.•The stressor´s timing should be considered in multiple stressors research.