Clostridioides difficile is a global one health threat, posing a significant risk to both humans and animals. This gut pathogen produces two cell types; a vegetative cell which is the disease-causing form and a spore, a highly resistant cell type that contaminates environments and facilitates disease initiation, dissemination, and re-infection. Our published work showed that cephamycin antibiotics could reduce spore numbers in C. difficile epidemic human isolates by targeting the spore-specific penicillin binding protein CdSpoVD. Of clinical relevance, we found that co-treatment of mice with the cephamycin cefotetan and the primary C. difficile infection treatment, vancomycin, prevented disease relapse. Here, we show that acquisition of a spore-specific protein, CdSpoCR, by C. difficile can block the ability of the cephamycins to reduce spore numbers. A survey of C. difficile genomes revealed that CdSpoCR is present in 10% of strains. TEM imaging and spore survival studies show a difference in spore morphology and resistance properties when this spore-specific protein is expressed. Finally, through sporulation assays, protein profiling and kinetic binding assays, we show that compound DL1 can target CdSpoCR, reducing spore numbers in a C. difficile animal strain. Our findings have uncovered a new antibiotic resistance mechanism that targets an unexpected part of the bacterial life cycle, and will help in developing an effective anti-sporulation therapeutic strategy encompassing a broader range of C. difficile isolates.