Value of the data•First detailed analysis of the prevalence of Clostridium perfringens and Clostridium difficile shedding by small animals (dogs and cats) in the Madrid region (Spain).•Detailed phenotypic and genetic data of recovered isolates is provided, which may be useful for comparison in future epidemiological surveys.•Given the recent emergence of antibiotic-resistant strains of C. difficle, information on the antimicrobial susceptibility profiles of the isolates obtained in this survey may be particularly valuable.