Seeds are a critical and limited resource for restoring biodiversity and ecological function to degraded and fragmented ecosystems. Cleaning and quality testing are two key steps in the native seed supply chain. Optimizing the practices used in these steps can ensure seed quality. Post‐collection handling of seeds can have a profound impact on their viability, longevity in storage, and establishment potential. The first section of this article describes seed cleaning, outlines key considerations, and details traditional and novel approaches. Despite the growth of the native seed industry and the need for seed quality standards, existing equipment and standards largely target agricultural, horticultural, and commercial forestry species. Native plant species typically have complex seed traits, making it difficult to directly transfer existing cleaning and quality standards to these species. Furthermore, in ecological restoration projects, where diversity is valued over uniformity crop standards can be unsuitable. We provide an overview and recommendations for seed quality testing (sampling, purity, viability, germinability, vigor), identity reporting, and seed transfer as well as highlight the need to implement internationally recognized standards for certification for native seeds. Novel and improved cleaning and testing methods are needed for native species from a range of ecosystems to meet the challenges and goals of the United Nations Decade on Ecosystem Restoration. The guidelines outlined in this article along with others in the Special Issue of Restoration Ecology “Standards for Native Seeds in Ecological Restoration” can serve as a foundation for this critical work.