This study shows that by-products obtained after cold-pressing oil production (flex oil cake, hemp oil cake, hull-less pumpkin oil cake) could be used as substrates for the sustainable and cost-effective production of lipase when cultivating Thermomyces lanuginosus under solid-state conditions (T = 45 °C, t = 9 days). Lipase showed optimum activity at T = 40 °C. The produced lipase extract was purified 17.03-folds with a recovery of 1% after gel chromatography. Three different batch experiments were performed in order to test the possibility of using the lipase in biodiesel production. Experiments were performed with a commercial, unpurified enzyme, and partially purified lipase with sunflower oil and methanol as substrates in a batch reactor at 40 °C. During the experiments, the operational stability of the enzyme was studied. The obtained results clearly showed that produced crude and purified lipase can be used for biodiesel production, but the process needs some additional optimization. As for operation stability, it was noticed that the commercial enzyme was deactivated after 30 h, while produced crude enzyme remained 8.25% of its activity after 368 h.