Hemp, flax and canola seed cakes are byproducts of the plant oil extraction industry that have not received much attention in terms of their potential use for human food instead of animal feed. Thus, the bioactivity profiling of these oilseed cakes is of interest. For their effect-directed analysis, planar chromatography was combined with several (bio)assays, namely 2,2-diphenyl-1-picrylhydrazyl scavenging, acetylcholine esterase inhibition, planar yeast estrogen screen, antimicrobial Bacillus subtilis and Aliivibrio fischeri assays. The streamlined high-performance thin-layer chromatography (HPTLC)-bioassay method allowed the discovery of previously unknown bioactive compounds present in these oilseed cake extracts. In contrast to target analysis, the direct link to the effective compounds allowed comprehensive information with regard to selected effects. HPTLC-electrospray ionization-mass spectrometry via the elution-head based TLC-MS Interface was used for a first characterization of the unknown effective compounds. The demonstrated bioactivity profiling on the feed/food intake side may guide the isolation of active compounds for production of functional food or for justified motivation of functional feed/food supplements.