This study evaluates the effects of four pretreatment methods: convection heating, microwaving, ultrasonication, and pulsed electric fields (i.e., PEF), on the chemical composition, color profile, functional properties, phenolic profile, antioxidant activity, fatty acid composition, and protein content of Nigella sativa L. (i.e., black cumin) cold-pressed cake. Seeds were subjected to each pretreatment prior to cold press extraction. Microwave, ultrasonication, and pulsed electric field pretreatments produced the lowest press cake yields (63.61–65.54%), statistically equivalent to one another. Also, the microwave-treated and control samples retained the highest protein content on a dry matter basis (30.81 and 30.79 g·100 g−1, respectively). Ultrasonication yielded the highest total phenolic and total flavonoid contents. Analysis of the press cake identified salicylic acid and catechin as the predominant bioactive compounds, suggesting potential antimicrobial and antioxidant applications. These findings provide evidence-based guidance for selecting Nigella sativa L. seed pretreatment strategies that at the same time optimize cold press oil extraction and the nutritional, functional, and bioactive value of the residual press cake. Thus, supporting its utilization as a sustainable by-product for food and feed applications.