Abstract: Second-to-second power imbalances stemming from renewable generation can have a large impact on the frequency regulation performance of isolated microgrids, as these are characterized by low inertia and, more commonly nowadays, significant renewable energy penetration. Thus, the present paper develops a novel frequency-constrained Energy Management System (EMS) that takes into account the impact of short-term power fluctuations on the microgrid's operation and frequency regulation performance. The proposed EMS model is based on accurate linear equations describing frequency deviation, rate-of-change-of-frequency, and regulation provision in daily microgrid operations. Dynamic simulations on a realistic CIGRE benchmark test system show the economic and reliability benefits of the presented EMS model, highlighting the need of incorporating fast power fluctuations and their impact on frequency dynamics in EMSs for sustainable isolated microgrids.