As a consequence of intense fishing pressure, fished populations experience reduced population sizes and shifts in body size toward the predominance of smaller and early maturing individuals. Small, early-maturing fish exhibit significantly reduced reproductive output and, ultimately, reduced fitness. As part of resource management and biodiversity conservation programs worldwide, no-take marine protected areas (MPAs) are expected to ameliorate the adverse effects of fishing pressure. In an attempt to advance our understanding of how coral reef MPAs meet their long-term goals, this study used visual census data from 23 MPAs and fished reefs in the Philippines to address three questions: (1) Do MPAs promote shifts in fish body size frequency distribution towards larger body sizes when compared to fished reefs? (2) Do MPA size and (3) age contribute to the efficacy of MPAs in promoting such shifts? This study revealed that across all MPAs surveyed, the distribution of fishes between MPAs and fished reefs were similar; however, large-bodied fish were more abundant within MPAs, along with small, young-of-the-year individuals. Additionally, there was a significant shift in body size frequency distribution towards larger body sizes in 12 of 23 individual reef sites surveyed. Of 22 fish families, eleven demonstrated significantly different body size frequency distributions between MPAs and fished reefs, indicating that shifts in the size spectrum of fishes in response to protection are family-specific. Family-level shifts demonstrated a significant, positive correlation with MPA age, indicating that MPAs become more effective at increasing the density of large-bodied fish within their boundaries over time.