Seagrass meadows are rapidly declining along coastlines worldwide, largely due to anthropogenic activities. Seed-based seagrass restoration can facilitate meadow recovery and enhance resilience to future disturbances. However, successful large-scale restoration relies on dispersing large quantities (hundreds to millions) of seeds. Aquaculture systems as a restoration tool (e.g., seagrass nurseries) can increase seed and plant yields while minimising impacts to donor meadows and maintaining genetic diversity in restored meadows. Zostera species have the capacity to produce a large number of seeds annually, and are deemed suitable for harvest and cultivation in nurseries. Here, we explore how temperature and light alterations affect flowering induction in Zostera muelleri, outside of the typical flowering season, by conducting manipulative laboratory experiments. To address this, we implement a systems biology approach by integrating photobiology and omics (transcriptomics and proteomics) to determine optimal environmental conditions for flowering induction and identify molecular pathways and biomarkers involved in flowering under the aforementioned conditions. This research will provide new knowledge on seagrass flowering biology with implications for increasing seed production efficacy under nursery conditions, ultimately enhancing our ability to successfully restore seagrass ecosystems.