This study was the first to compare the structural features, functional properties and in vitro digestibility of two protein concentrates produced from defatted sunflower meal via two different three-stage processes (chlorogenic acid removal-alkaline extraction-isoelectric precipitation versus chlorogenic acid removal-alkaline extraction-ultrafiltration; concentrates termed AI-SPC and AU-SPC, respectively). Compared with AI-SPC, AU-SPC with a darker brown color had much higher protein recovery yield and purity, much higher solubility at pH 4–7, higher oil-holding capacity, greater emulsifying and foaming capacities at pH 7 and 9, and slightly lower foaming capacity at pH 3. The bioavailability was higher for AU-SPC after oral-gastric-intestinal digestion. Moreover, AI-SPC occurred as clumps/lumps of particles, whilst AU-SPC appeared as flat blocks with continuous surfaces. AU-SPC was more negatively charged, and had a smaller particle size, less β-sheet, more β-turn, slightly more α-helix structure. These results confirmed the close relationship between protein production methods and its functional properties and digestibility.