Seagrass meadows are an important habitat for Testudines (sea turtles) and Sirenia (dugong and manatee) megaherbivores. Megaherbivores can influence the structuring of seagrass meadows; for example, foraging patterns have been found to relate to seagrass phenological strategy. However, as these observations are derived from uncontrolled field studies, it is unclear whether grazing drives such changes or if the changes are related to other factors (e.g., temperature, tidal depth, light). In the present study, a mesocosm experiment was designed to test the impacts of grazing on metrics of flowering of Zostera muelleri over two consecutive flowering seasons. Prior to each flowering season, plants were cropped to 3 cm and 1 cm lengths to represent turtle and dugong grazing, respectively. This study measured the timing of flowering, the number of flowering shoots, the height of the flowering shoot, and the number of spathes (sheathing bracts containing seeds) per flowering shoot in each replicate (n = 5) weekly. Cropping had no significant influence on the timing of flowering (i.e., number of days to first and peak flowering) indicating that it is not a trigger for flowering. However, cropping significantly reduced the maximum density of flowering shoots and spathes, which was proposed to be due to resource allocation differences between clonal growth and flower production. A reduction in the flowering ratio was observed in both cropped plant groups and the relatively high density and the ratio of flowering observed in the 1 cm group indicate that the plant was adapting to cope with stress. Morphology of flowering (i.e., the maximum height of flowering shoot and the maximum number of spathes per flowering shoot) was not significantly affected by cropping and these two variables were strongly correlated. The results suggest that cropping can influence the overall flowering densities in a season but not the timing of flowering. This study demonstrated that cropping prior to the flowering season can reduce the expected production of spathes in seed nurseries and suggests it may be beneficial to consider megaherbivores in seed-based restoration activities.