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 toxin producing, 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 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 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 protein is expressed, suggesting that these spore phenotypes can be altered by the acquisition of genes from other, unrelated bacteria. Finally, through sporulation assays and fluorescent polarisation 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.