Methods for making crosslinked material, such as collagen-based material, and bioprosthetic devices. The crosslinked material includes hydroxyl groups, carboxyl groups, and amine groups prior to crosslinking. The methods include removing at least a portion of the zero-length ester crosslinks in a crosslinked material and/or blocking at least a portion of the amine groups that are reactive with carboxyl groups and form zero-length crosslinks.