Secretory structures in plants play a crucial role in producing bioactive compounds. Despite the potential of the Swartzia genus, comprehensive studies in this context are still scarce. Swartzia is a legume tree (Fabaceae) that occurs in the Brazilian Atlantic Forest, a biodiversity hotspot, and includes species such as Swartzia flaemingii. Therefore, we aim to achieve: (1) identify and characterize the key secretory sites responsible for saponin production in S. flaemingii leaflets; (2) confirm the presence of saponins in S. flaemingii leaves by comparing them with known chemical profiles of other Swartzia species; (3) assess the potential hemolytic and cytotoxic effects of crude leaf extracts. Our investigation unveils the presence of phenolic idioblasts, mucilage cells, and articulate laticifers, which play pivotal roles in defense and adaptation. Notably, we report the first‐ever ultrastructural details of laticifers in a legume species. Additionally, oleanane‐type saponins were identified in the leaves, giving insights about the chemotaxonomic profile of Swartzia. The crude extracts show low cytotoxicity levels, showcasing as a promising alternative source of saponins. This investigation reinforces the importance of conserving plants in threatened regions like the Atlantic Forest, a global biodiversity hotspot facing substantial anthropogenic pressures.