Food loss and waste, about 30% of human-consumable food production, pose challenges to safety, the economy, and the environment. A significant portion includes discarded fruit parts, notably seeds. Pequi fruit seeds contribute to agro-industrial waste due to their intricate structure and thorns, raising environmental concerns. Prior research shows promise in utilizing pequi seeds (PS) for bioenergy through pyrolysis and gasification, but comprehensive torrefaction optimization investigation is lacking. Furthermore, PS contains 40–50% extractives, constituting a potential feedstock for biodiesel and enhanced biorefinery value. Despite literature on extractive valuation, studies often neglect residual biomass and biorefinery integration. This study fills the gap by evaluating the torrefaction of post-extraction residual biomass (PSW) and comparing it to PS. Using Response Surface Methodology (RSM), torrefaction conditions are optimized, evaluating Soxhlet extraction impact on raw (PS) and de-oiled pequi seeds (PSW) across scenarios: prioritizing biochar quality (S1) and simultaneously evaluating biochar quality, energy requirements, and potential CO2 retention (S2). Biochar parameters include solid yield, bulk density, proximate, ultimate, and energetic properties. Torrefied pequi seeds show superior biofuel properties, with up to 21% HHV enhancement for PSW, including increased energy content and substantial CO2 emission reductions compared to fossil fuels. RSM provides statistically significant models (reduced quadratic, reduced cubic, and reduced 2FI), with R2 > 0.9762 for the assessed biochar outcomes. The study identifies PS torrefaction at 274 °C and 42 min as optimum in S1, resulting in biochar (CH1.30O0.33) with a 76.18% energy yield and HHV of 24.11 MJ kg-1. In S2, PS is also optimal, with ideal torrefaction at 265 °C and 31 min, providing biochar (CH1.39O0.36) with an 82.11% energy yield, HHV of 23.83 MJ kg-1, and a 188.65 kg CO2eq (by substituting diesel as