Knowledge on seed ecology is foundational for effective seed‐based restoration including seedling production, direct seed sowing, topsoil transplant, and natural regeneration. Consequently, quantifying available knowledge and biases in seed‐based research allows practitioners to better plan and implement seed‐based restoration programs and identify research priorities. Using a systematic review comprising 45 papers, 401 species, and 2,415 case studies, we provide an overview of seed ecology research in the Pantanal, the world's largest tropical wetland. We identified geographic, taxonomic, and ecological biases, as well as knowledge gaps in seed functions including production, dispersal, dormancy, germination, predation, and stress tolerance. Studies concentrated near large cities resulting in extensive unexplored sites in central Pantanal, in Paraguay, and in Bolivia. Unexpectedly, the most studied species were conducted with dry‐fruited, terrestrial forbs, or shrubs with autochoric or zoochoric dispersal syndromes. Seed banks, stress tolerance, and dispersal were the most studied topics, whereas studies on dormancy and seedling establishment remain rare. We also found disproportionate research interest across the angiosperm tree of life with many examples of underrepresented and overrepresented families. Altogether, persistent knowledge gaps in seed‐based research in the Pantanal hinder upscaling restoration programs and consequently the likelihood of achieving the targets of UN Decade of Ecosystem Restoration. We propose an integrated agenda consisting of a series of orchestrated actions to overcome such barriers, close biodiversity knowledge shortfalls, and promote successful large‐scale restoration programs in the Pantanal.