The capacity of four formulations of natural deep eutectic solvents (NDESs) for extraction of canola protein was compared to alkaline extractions at pH 12 and pH 9. NDESs were prepared with a 1:2:1 ratio of choline chloride/d-sorbitol, glycerol, d-glucose or urea/water. The urea formulation showed the lowest viscosity and density and highest polarity; and extracted a bright-yellow isolate with extraction efficiency of 52.89% and protein content of 84.03%. The rest of NDESs extracted light-green isolates with efficiencies of approximately 44%. Furthermore, All NDESs offered lower extraction efficiencies than pH 12 (68.34%, dark-green isolate) but higher than pH 9 (39.14%, yellow isolate). Molecular analysis via SE-HPLC and SDS-PAGE showed the presence of cruciferins and napins in all isolates, but higher napin contents for NDES isolates with cruciferin-to-napin ratios of around 60:40. NDESs also altered the secondary and tertiary structure of the protein to a lesser extent. The functionality analyses at pH range of 3–7 revealed better solubility for pH 9 (72.09%–39.35%) and glycerol formulation (68.61%–39.05%) isolates; and better foaming properties for all NDES isolates, possibly due to their higher napin contents. NDES isolates also showed better emulsifying properties at pH 5 and 7, while alkaline isolates produced more stable emulsions at pH 3, possibly due to the better solubility of their cruciferins at pH 3. Overall, NDES isolates offered higher extraction efficiencies and a close functionality compared to pH 9 isolate, better color and functionality than pH 12 isolate, and better preservation of native protein structure compared to both alkaline treatments.