The Philippines has lost nearly 70% of its natural mangrove cover since the early 1900s. As a result, large investments have been made to restore mangrove forests and the many ecosystem services that they provide. Most of these restoration efforts have been through outplanting of Rhizophora sp. seedlings, many of which have failed because the proper hydrological and ecological conditions were not properly assessed. Other afforestation projects involved planting seedlings in inappropriate places (e.g., seagrass beds, mudflats) that resulted in replacing one valuable ecosystem with another. The aim of this research was to investigate the growth of 3-, 9-, and 21-year-old afforested stands of Rhizophora spp. mangrove forest. We also investigated the impact of these plantations on local seagrass beds. The total aboveground biomass was 42.6, 74.4, and 111.7 Mg ha−1 for the 3-, 9-, and 21-year-old mangrove stands, respectively. Seagrass bed cover decreased under the closed canopy of the mangrove due to reduced photosynthetically active radiation and competition for growing space. This study shows that mangroves can grow to some extent on seagrass beds, though mangrove planting in these areas could eventually lead to seagrass loss. Thus, mangroves should not be planted in areas that are naturally occupied by other ecologically important ecosystems. The purpose of mangrove restoration should be clear and efforts should be focused on formerly deforested or degraded areas. Additional studies are needed from different locations to understand how mangrove planting in seagrass beds impacts growth performance and ecological functions of the latter ecosystem.