Marine phytoplankton regulate oceanic nitrogen cycling through tightly coordinated diel metabolic programs, yet how these temporal architectures respond to long-term environmental change remains poorly understood. Most projections of future ocean biogeochemistry assume physiological acclimation while overlooking the potential for evolutionary adaptation to reorganize metabolic timing. Here, using a multi-year experimental evolution approach with the marine diatom Phaeodactylum tricornutum, we investigated how adaptation to elevated CO₂, warming, and their combination reshapes diel nitrogen metabolism. Long-term adaptation produced extensive reorganization of nitrogen allocation and recycling, characterized by altered metabolite dynamics and enhanced nighttime nitrogen processing. Transcriptomic analyses of 28 nitrogen-metabolism genes revealed widespread phase rewiring, with many urea-cycle, nitrogen-assimilation and transport genes shifting their peak expression timing relative to the ambient regime. These transcriptional changes were coordinated with metabolite-level adjustments, indicating a temporal reprogramming of nitrogen metabolism rather than simple changes in pathway activity. Network analyses further showed that although adaptation modified patterns of module-level coordination, overall synchronization among nitrogen-metabolism pathways remained largely conserved. Together, our findings demonstrate that evolutionary adaptation can reshape the temporal organization of marine nutrient cycling by rewiring metabolic and transcriptional rhythms. Incorporating evolutionary changes in diel regulation may therefore be essential for predicting future ocean ecosystem functioning under global change.