The spleen, traditionally associated with blood filtration and immune surveillance, has recently been recognized for its role in systemic lipid metabolism and potential influence on cancer development and progression. This study investigates effects of dietary supplements, specifically conjugated linolenic acids from pomegranate seed oil and bitter melon extract, on the fatty acid (FA) composition of the spleen in the context of cancerous processes. Advanced methods, including gas chromatography–mass spectrometry and silver ion-impregnated high-performance liquid chromatography, were employed to analyze the spleen’s FA profile. Our research uncovered that dietary supplementation leads to alterations in the spleen’s FA profile, especially under the carcinogenic influence of 7,12-dimethylbenz[a]anthracene. These changes did not align with a simple protective or anti-carcinogenic pattern, as previously suggested in in vitro studies. We observed shifts in conjugated FA isomer concentrations and variations in desaturase activities, suggesting disrupted lipid metabolism in cancerous conditions. The findings underscore the spleen’s vital role in lipid metabolism within the body’s systemic health framework, highlighting the complexity of dietary supplements’ impact on FA profiles in the spleen and their potential implications in cancer progression and treatment. This study adds valuable insight into the complex interplay between diet, disease, and metabolic regulation, particularly in cancerous environments.