Diisopentyl phthalate (DiPeP) is a plasticizer with significant offer and application in Brazilian industries. This is attributed to its origin, which is closely linked to the refining process of sugarcane for ethanol production in the country. In this work, we developed a model for trophic exposure to environmentally relevant doses (5, 25, and 125 ng/g of DiPeP) to identify possible target tissues and toxic effects promoted by subchronic exposure to DiPeP in a Neotropical catfish species (Rhamdia quelen). After thirty days of exposure, blood, liver, kidney, brain, and muscle were collected and studied regarding DNA damage in blood cells and biochemical analyses. The kidney was the most affected organ, as in the head kidney, genotoxicity was evidenced in all groups exposed to DiPeP. Besides, the caudal kidney showed a reduction in the superoxide dismutase and glutathione peroxidase activities as well as a reduced glutathione concentration. In the liver, exposure to 125 ng/g of DiPeP increased glutathione S-transferase activity and reduced glutathione levels. In muscle, acetylcholinesterase (AChE) was reduced. However, in the brain, an increase in AChE activity was observed after the exposure to lowest doses. In contrast, a significant reduction of brain AChE activity after exposure to the highest dose was detected. The pronounced genotoxicity observed in head kidney cells is of concern, as it may compromise different functions performed by this organ (e.g., hematopoiesis, immune and endocrine functions). In our study, DiPeP proved to be a compound of environmental concern since we have evidenced its nephrotoxic and neurotoxic potential even in low doses.