Enzyme-deantigenated equine bone (EDEB) and anorganic bovine bone (ABB) are two xenografts made non-antigenic through different processing methods. This study aimed to characterize them for the presence of native bone collagen and other proteins and to compare their histomorphometric outcome when they were used to graft post-extractive sockets. The records of 46 patients treated with EDEB (n = 22) or ABB (n = 24) and followed-up for at least four months after delayed implant placement, were retrospectively collected. Samples of EDEB and ABB were analyzed using Attenuated Total Reflection Fourier Transform Infrared and Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis for the presence of collagen and other proteins. For histomorphometric analysis on bone specimens, newly formed bone and residual biomaterial percentages were calculated. Results of the present study show that EDEB contains type I bone collagen in its native conformation, while no proteins were detected in ABB. Grafting EDEB resulted in a significantly greater quantity of newly formed bone and less residual biomaterial. Our findings suggest that the manufacturing process can greatly affect the graft behavior and a process preserving collagen in its native form may favor bone tissue regeneration.