Fats derived from coffee by-products, i.e., coffee pulp (CP), could constitute a valuable source of bioactive lipids for neuroprotective nutraceutical development. Sustainable recovery of these lipids and comprehensive compositional profiling using high-throughput lipidomics are essential steps in valorizing CP waste streams. This work aimed to explore the impact of the ethanol-modified supercritical carbon dioxide (EtOH-scCO₂) extraction technique on the profile of recovered lipid fractions under several extraction conditions (45 and 65 ºC; 20 and 30 MPa; and 5 and 10% w/w co-solvent) by UHPLC/ESI-timsTOF, alongside conventional Folch extraction. Profiling analysis revealed that the Folch method yielded a higher number of lipids (266) compared to EtOH-scCO₂ (from 249 to 263), but the overall lipid abundance was decreased. Glycerolipids and triacylglycerols were the dominant categories and classes, respectively, across all groups. Differential analysis demonstrated that glycerophospholipids, phosphatidylinositols, and sulfoquinovosyldiacylglycerol 16:0_18:3 lipid exhibited the most significant expression differences at the category, class and species level, respectively. EtOH-scCO₂ extraction, in comparison with the Folch method, favored the extraction of long-chain lipids containing more double bonds, with lower EtOH proportion (5%) resulting in a longer chain and a higher unsaturation degree. Multivariate analysis (PCA, PLS-DA, and hierarchical clustering) showed a clear different lipid profile between EtOH-scCO₂ and Folch extracts. Moreover, EtOH-scCO₂ extracts were further distinguished according to EtOH percentages, with lower ethanol content (5%) diverging most from Folch extracts, which reflected a tunable extraction selectivity driven by the relatively lower polarity of the supercritical phase. This trend was further supported by the significantly high correlation between EtOH and lipid species, highlighting the notable contribution of EtOH in lipid extraction. Overall, these results suggested that the EtOH-scCO₂ extraction offered a promising and selective approach for obtaining extracts enriched in long-chain polyunsaturated lipids from CP, with a prospective ability to enhance nerve function and brain health. These findings guide the targeted recovery of specific lipid species from coffee by-products for high-value applications.