Background: Current drug for the treatment of endometriosis is not able of completely cure and significant side effects hinder the continuation of treatment. So, the search for new drug candidates is necessary, and the use of plants extracts is highlighted. Babassu oil and copaiba oilresin have several therapeutic properties. We investigated the in vitro effects of two nanoemulsions containing babassu oil (Orbignya speciosa) (SNEDDS-18) and/or copaiba oilresin (Copaifera langsdorffii) (SNEDDS-18/COPA) on cultured human eutopic endometrium stromal cells from endometrial biopsies of patients without (CESC) and with (EuESC) endometriosis, and human stromal cells from biopsies of endometriotic lesions (EctESC). Methods: CESC, EuESC and EctESC were established and treated with SNEDDS-18 and SNEDDS-18/COPA to evaluate its effects on cytotoxicity, cell morphology, proliferation, and signaling pathways. Results: After 48 hours incubation with SNEDDS-18 and SNEDDS-18/COPA, cell viability and proliferation were inhibited, especially in EctESC. The lowest concentration of both nanoemulsions reduced cell viability and proliferation and breakdown the cytoskeleton in EctESCs. After 24h treatment it was observed a decrease in IL-1, TNF-α, and MCP-1, and an increase in IL-10 production. Conclusions: Both nanoemulsions can affect the endometriotic stromal cell behaviors, thus revealing two potential candidates for new phytotherapeutic agents on the management of endometriosis.