Sediment fertilization is recommended for improving seagrass restoration efforts, but few studies have evaluated the efficacy of such practice. Increasing storm frequency due to global change could lead to greater sediment mobilization. Understanding how this alteration will interact with fertilization to affect transplants is essential for future restoration planning. We examined the individual and combined effects of nutrients (ambient vs. repeated addition) and burial (control vs. increased frequency and intensity) on the performance and biomass partitioning of transplants of the seagrass Cymodocea nodosa at two sites within a north-western Mediterranean meadow. Fertilization stimulated the production of shoots, total biomass, and branching. Burial increased leaf sheath length in one site while reduced shoot number, leaf number, leaf sheath length, total biomass, net shoot gain, and root-to-shoot ratio in the other site. Regardless of the site, fertilization and burial interaction reduced the length of vertical internodes and horizontal rhizomes, and the net shoot gain. Our research demonstrates that sediment fertilization ensures rapid colonization of restoration sites, providing C. nodosa plants up to eight times larger than controls in one growing season. However, it also indicates that interaction of increased burial and nutrients reduced the gain in terms of vegetative expansion and depressed vertical growth, making plants more vulnerable to subsequent disturbances. Therefore, seagrass restoration practitioners should account for changes in sediment elevation at transplanting sites when planning restoration programs and carefully evaluate the opportunity of applying fertilizers in sites subjected to greater sediment accumulation to avoid failure.