Climate change profoundly modifies the global ocean potentially threatening marine ecosystems. Under the Paris Agreement, the international community aims to limit global warming by achieving net-zero CO₂ emissions, through the balance between CO₂ emissions and removals. Yet, the response of the ocean to net-zero, and associated impacts, remains poorly understood. Prevailing Global Warming Level (GWL) approaches applied to analyse the impacts of climate change on the ocean overlook committed changes arisen after emissions cessation. Using the CNRM-ESM2-2 Earth system model, we perform 300-year net-zero simulations spanning +1.1 °C to +5 °C above pre-industrial levels, to investigate the ocean responses to CO₂ emissions cessation, and how they depend on the warming level at which net-zero emissions is reached. Focusing on sea surface temperature (SST) and marine heatwaves (MHW) – key threats for marine ecosystems – we find substantial departures from transient responses throughout the 300-years of stabilization. At the Paris Agreement targets of +1.5 °C and +2.0 °C above pre-industrial levels, 26 % and 32 % of the global ocean, respectively, exhibit simultaneous increases in SST mean and variance as compared to transient warming simulations. These changes cover particularly the high latitudes and Southern ocean. MHW reorganize rapidly after emissions cease, with a poleward shift in frequency, declines in the tropics, and overall sustained intensity. Altogether, these non-transient responses indicate that standard GWL approaches underestimate MHW reorganization by decades to centuries. Net-zero simulations are therefore critical for robust projections of marine ecosystem risk at stabilized global warming levels.