The waste, or by-product that remains after the cold pressing of the oilseeds, is called oil cake. Due to the residual oil content, high amount of proteins, dietary fibers, minerals and other bioactive compounds, oil cakes are recognized as a valuable raw material in the production of high-value products, or as a nutritional dietary supplement. In this paper, pumpkin and flaxseed oil cakes were analysed, before and after fermentation with white rot fungus, Trametes versicolor, and thermophilic fungus, Humicola grisea, using solid state technology. Contents of dry matter, ash, total and extractable proteins, ether extract, fibers (NDF, ADF, ADL), extractable sugars, and total organic carbon were determined in untreated oil cakes and after 10 days of fermentation. Concentration of simple sugars was analyzed every day of cultivation. Based on the obtained results, it was concluded that after processing pumpkin oil cake with Trametes versicolor, contents of ether extract and fibers are significantly reduced, while processing with Humicola grisea does not have significant impact on those parameters, but causes an increase in protein content. After processing of flaxseed oil cake with either of the two microorganisms, an increase in the protein and extractable sugars content was observed, while contents of fibers and ether extract decreased. Based on the analysis of individual simple sugars, it was found that both microorganisms have the ability to break down polysaccharides, simultaneously releasing monosaccharides and oligosaccharides.