The application of walnut-based dyes in leather dyeing represents a less polluting process compared to the use of synthetic dyes; however, it still requires the evaluation and treatment of the generated effluents. The present study evaluated the efficiency of COD removal through the application of electrocoagulation and ozonation processes for the treatment of effluents generated during the dyeing of paiche skins using a walnut leaf-based dye. Subsequently, bioassays using Lactuca sativa seeds were conducted to assess the toxicity of both treated and untreated effluents, as well as the natural walnut-based dye and reference synthetic dyes. Optimal conditions for the electrocoagulation process were identified at a treatment time of 30 min and a current intensity of 7 A, achieving a COD removal efficiency of 51.67%. The application of ozonation as a complementary process to electrocoagulation resulted in an additional maximum removal of 12.51%. The bioassays indicated a reduction in toxicity in effluents treated by electrocoagulation compared to the untreated effluent. Regarding the dyes, the natural walnut-based dye exhibited higher toxicity than the synthetic dyes; however, this toxicity is associated with the active compound juglone, which has known phytotoxic activity.