Tissue-engineered small intestinal implants are being widely investigated as a potential treatment for children with short bowel syndrome, yet are currently limited by their growth potential and relatively low surface area. To address this gap in the field, several investigators have utilized whole organ decellularization of the small intestine as a platform for subsequent growth of intestinal tissue. However, such scaffold-cell constructs require sterilization as a prerequisite for implantation, and the effects of the different pathogen-clearance techniques used on the tissue architecture remains unknown. The effects of four different published protocols for pathogen clearance of decellularized intestine, namely 0.1% peracetic acid (PAA), 0.18% PAA +4.8% ethanol (EtOH), 0.08% PAA +1% hydrogen peroxide (H2O2), and ultraviolet (UV) sterilization were compared using qualitative and quantitative techniques to assess changes to the extracellular matrix, cytocompatibility, and biocompatibility. All methods of sterilization of decellularized intestine were found to be equally effective and each method had similar histologic and scanning electron microscopy appearance of the sterilized tissue. In addition, collagen and glycosaminoglycan quantities, and the ability to support cell growth were similar among all methods. This study provides insights into the change in crypt villous architecture of the extracellular matrix with all sterilization techniques studied. Our findings demonstrate that sterilization affects the microarchitecture significantly, which has not been well accounted for in studies to date, and we were unable to identify a single best agent to achieve tissue sterilization while preserving the microarchitectural features of the tissue.