To develop novel processes for valorizing agro-industry side-streams, canola (Brassica napus) oil press cakes (CPC) were treated with lactic acid bacteria, carbohydrase, and protease. Altogether 29 protein-rich liquid fractions were obtained, of which the composition was analyzed using chromatographic and mass spectrometric methods. A clear association was revealed between the treatments and phenolic profile. Applying certain lactic acid bacteria enhanced the release of sinapic acid, sinapine, glycosylated kaempferols, and other phenolic compounds from CPC. Co-treatment using protease and Lactiplantibacillus plantarum was effective in degrading these compounds. The fraction obtained after 16 h of hydrolysis (with Protamex® of 2% dosage) and 48 h of fermentation (using L. plantarum) contained the lowest phenolic content (0.2 g/100 g DM) and a medium level of soluble proteins (78 g/100 g) among all samples studied. The fractions rich in soluble proteins and low in phenolics are potential food ingredients with improved bioavailability and sensory properties.