In recent decades, the global intensification of marine heatwaves has impacted several ecosystems and species, including the endemic Mediterranean seagrass Posidonia oceanica. However, the scarcity of research in Eastern Mediterranean meadows, where historical and present thermal conditions differ from those of the Western Mediterranean, hampers our ability to draw comprehensive conclusions regarding the species' response to elevated sea temperatures. Here, we studied flowering patterns of P. oceanica meadows (3–15 m depth) of the Greek seas and assessed their potential association with marine heatwaves, while also examining the effects on plant growth associated with the transition from vegetative to sexual reproduction. To do so, we reconstructed flowering patterns from 2007 to 2021 across 58 meadows using lepidochronology and estimated summer marine heatwave metrics and categories using satellite sea surface temperature. The results revealed that flowering, while sporadic in most meadows (mean flowering frequency: 0.15), it was triggered by strong (Category II) summer marine heatwaves and a cumulative intensity exceeding 30°C days. Nevertheless, flowering density was low (mean flowering density: 11 inflorescences m−2) and not fuelled by frequency, intensity, or duration of marine heatwaves. Despite the potential long‐term benefits of sexual reproduction, annual rhizome production of flowering shoots decreased 1.5‐fold for at least 2 yr postflowering. This study uncovers the susceptibility of Eastern Mediterranean P. oceanica meadows, akin to their western counterparts, to marine heatwaves induced stress and its effects on reproductive strategies, raising concerns about the prospective plant growth and reproductive fitness to the escalating trend in marine heatwaves.