The development of rapid and efficient conversion routes is essential to improve the feasibility of microalgae-based biodiesel. This study investigates the nonlinear enhancement of microwave-assisted in-situ transesterification using the marine diatom Skeletonema costatum as a model feedstock. A Response Surface Methodology (RSM) based on a Box–Behnken Design was applied to evaluate the effects of microwave power (100–600 W), reaction time (2–8 min), and microalgae-to-solvent ratio (1:30–1:50 g/mL) on biodiesel yield under microwave irradiation. The results revealed a pronounced nonlinear response among process variables, with the quadratic effect of microwave power emerging as the dominant factor influencing biodiesel yield. The optimal condition yielded 96.169% biodiesel (dry biomass basis) at 600 W, 5 minutes, and a 1:50 (g/mL) ratio. GC–MS analysis confirmed a methyl ester content of 79.53%, predominantly hexadecanoic acid methyl ester (73.61%), demonstrating the suitability of marine diatoms as promising biodiesel feedstocks. Microwave irradiation significantly intensified the transesterification process by reducing reaction time while maintaining high conversion efficiency. This study is limited to laboratory-scale experiments and a defined operational window, and further work is needed to assess scalability, energy efficiency, and broader process conditions. Nevertheless, the findings provide practical insight into fast and simplified biodiesel production from marine microalgae. The main contribution of this work lies in demonstrating nonlinear process enhancement under microwave irradiation and providing a systematic framework for understanding microwave-driven in-situ transesterification in marine diatoms.