The sustainable extraction of secondary metabolites from Brassica agro-industrial by-products often involves the use of high concentrations of ethanol, and/or high temperatures, which tends to decrease the efficiency of protein extraction (yield, profile, etc.). To understand the limits of the combination of these two extraction processes, aqueous ethanol extraction of secondary metabolites (e.g., phenolic compounds and glucosinolates) from Brassica carinata defatted meal was optimized using Response Surface Methodology. The validated models predicted that aqueous ethanol extraction of defatted Carinata meal, with a low aqueous EtOH concentration (22% EtOH) at moderate Te (50 °C), enables the efficient recovery of secondary metabolites (sinapine = 9.12 ± 0.05 mg/gDM, sinigrin = 86.54 ± 3.18 µmol/gDM) while maintaining good protein extractability (59.8 ± 2.1%) from successive alkaline extractions. The evaluation of functional properties of the resulting protein isolates revealed that aqueous extraction, under optimized conditions, improves foaming activity while preserving emulsion ability.