Aqueous extraction of oil and protein from soybean flour was investigated to elucidate the mechanisms involved. The process variables investigated were: particle size, temperature, time, pH, power input, solid-to-liquid ratio, use of several extraction steps, and the use of preliminary heat treatment prior to the extraction. Protein and oil extraction yields were shown to be closely related, both depending on the level of disruption of cell wall. Experimental investigations show that protein extraction from the disrupted cells follows a solubilization/diffusion mechanism. Conditions that favour protein extraction—i.e., temperature below the level causing denaturation, pH away from the isoelectric point, and use of several extraction steps—generally favour oil extraction. However, the mechanisms governing protein extraction rates are quite different from those governing oil extraction rates. The extraction mechanisms are also elucidated in the context of the cell structure, and the response to different extraction parameters form the basis for the process design and optimization.