Agroforestry is recognized as a friendly land-management practice because it can contribute to improve soil productivity, biodiversity conservation, ecosystem functions, climate change mitigation, landscape connectivity and the delivery of ecosystem services, optimizing livelihood benefits for people. The Atlantic Forest, a worldwide biodiversity hotspot, which presents large areas in natural regeneration and a promising scenario for ecological restoration has great potential for agroforestry. According to Brazilian legislation, the agroforestry conducted on remnants of Atlantic Forest depends on previous environmental authorization regarding both the vegetation management and the commercialization of native flora products. Although Brazilian legislation provides incentives for agroforestry, there are important barriers to its development regarding to the vegetation management for production, processing (enforcement of health and sanitation laws), and trading of timber and non-timber products. In the Rio Grande do Sul, the procedures for obtaining environmental authorization concerning the management and trading of native plants were too bureaucratic, unattractive, and infeasible for small rural landowners because the environmental legislation was not translated into effective public policies. Since the agroforestry and extraction of native flora products needs to comply with legislation and the key point is to guarantee the legal and sustainable origin of the products, and the management carried out, the appropriate procedure for the regularization of such practices is a certification of forest management. The SEMA’s agroforestry certification (SAC) is a simplified procedure to legal compliance and sustainable management of native vegetation and mainly attends family farmers, indigenous peoples, maroons, and traditional populations. Until September 2019, nearly 130 landowners requested the SAC from 65 municipalities of Rio Grande do Sul. According to the applicants, around 99% of rural properties are considered small, ranging from 1.3 to 156 ha. Altogether, they add up to almost 380 ha of agroforestry in anthropic areas, some of them degraded by intense historical land use. The extraction of fruits and seeds and the planting of native tree species (59% and 48%, respectively) were the most mentioned agroforestry management by the applicants. The main products or species of interest mentioned were fruits and heart of palm from Euterpe edulis (52%), fruits of Citrus spp. (51%), native timber (49%), non-native fruits (44%), native Myrtaceae fruits (39%), other native fruits (32%), banana crops (29%), Yerba-mate (26%), non-native timber (16%), other non-native plants (9%), ornamental plants (9%), Butia catarinensis fruits (7%), and Butia odorata fruits (2%). The SAC has brought stakeholders (farmers, technical assistants, and researchers) closer to the environmental agency, creating a broad new regional agenda on agroforestry, and a myriad of conservation opportunities. The strengthening of agroforestry-support policies must be an important conservation strategy in the Atlantic Forest. However, to carry out such policies, it is necessary to create conditions and incentives beyond the legislative scope, translating the legal provisions to procedures and actions.