Clostridium perfringens represents an important cause of sudden death and acute disease in cattle. Although diagnostic investigations focus on organs or intestinal contents collected from animals, field experience suggests that feed management may play a central role in the occurrence of clostridial problems at farm level. In the clinical investigations considered in this study, sampling was triggered by sudden death or clinical signs compatible with clostridiosis. The diagnostic approach was extended to feed matrices and management-related risk factors, with particular attention to feed storage, preservation, and distribution. To evaluate and compare the detection patterns of C.perfringens toxins, an ELISA commercial kit was used to test 52 field samples collected during diagnostic investigations and monitoring activities. The dataset included 34 animal organ samples (kidney, spleen, liver, intestine, lung, and heart) and 18 food/feed samples. Samples were tested for the presence of alpha, beta, and epsilon toxins, as well as C.perfringens antigen. Toxin detection was more frequent in food/feed matrices (55.6%) compared to organ samples (32.4%). Epsilon toxin showed the most pronounced matrix-associated difference, being detected significantly more often in food/feed matrices (44.4%) than in organ samples (11.8%) (p = 0.014). This finding suggests that C.perfringens may complete its life cycle and fully activate its metabolic and toxigenic potential within feed prior to ingestion by the host. Among food matrices, unifeed samples showed a 53.3% overall toxin positivity rate. In organs, toxin positivity was most frequently observed in kidney (44.4%), lung (50.0%), and spleen (37.5%), predominantly involving beta and epsilon toxins, while liver samples were consistently toxin-negative. A farm-specific autogenous vaccine will be prepared from outbreak-associated C.perfringens isolates recovered from clinically affected animals. Strains will be selected on the basis of culture results and PCR detection of toxin genes, ensuring inclusion of beta- and epsilon-toxin antigens that are absent from commercial vaccines targeting alpha toxin alone.