Coastal and estuary ecosystems are increasingly subjected to compound events, where multiple extreme events such as marine heatwaves (MHW) and hypoxia occur simultaneously. Given the fundamental role of temperature and oxygen in biological processes, the combined alteration of these parameters is often expected to have non-linear effects on organisms. However, the potential for an extreme temperature event to elicit a different response than gradual warming when combined with hypoxia remains understudied. Therefore, we examined the within-generational response to simultaneous hypoxia and MHW, and the transgenerational plastic responses during the recovery phase of the foundational marine copepod species, Acartia tonsa. In more detail, we measured survival, egg production rates, metabolic rates and upper thermal limits on mature males and females (F1) following a five-day exposure to the isolated and combined effects of hypoxia and a MHW, and on their offspring (F2) placed back in a control condition for their whole development, once they reached adulthood. Surprisingly, we observed only synergistic effects for F1 males’ upper thermal limits and no strong carry-over effects in the recovering F2 coming from the parental combined condition. However, MHW had a dominant effect on the physiology of A. tonsa, decreasing survival, increasing metabolic rates and causing strong carry-over effects on F2 individuals’ survival. These results indicate that potential cross-protection mechanisms between the two stressors were at play, enabling copepods to face the deletarious effects of MHW when exposed simultaneously to hypoxia. This supports the importance of looking at the impact of compound events on marine organisms.