Decellularized esophageal matrices are ideal scaffolds for esophageal tissue engineering. Unfortunately, in order to improve transplantation possibilities, they require modification to reduce their degradation rate and immunogenicity. To date, no modifying agent has been approved to overcome these limitations. The objective of this study was to evaluate the ability of silver nanoparticles (AgNPs) to improve the structural stability and biocompatibility of decellularized rat esophagi. AgNPs have the advantage over currently used agents in that they bind with collagen fibers in a highly ordered manner, via non-covalent binding mechanisms forming multiple binding sites, while other agents provide only two-point connections between collagen molecules. Rat esophagi were decellularized, loaded with 5 μg/mL of AgNPs (100 nm), and then treated with an immobilization-complex buffer composed of ethyl carbodiimide hydrochloride and N-hydroxysuccinimide (EDC/NHS). Then, they were evaluated in terms of ultra-structural morphology, water uptake, in vitro resistance to enzymatic and thermal degradation, indentation strength, in vitro anti-calcification, cytocompatibility with rat bone marrow derived stromal cells (rat-BMSCs), angiogenic properties, and in vivo biocompatibility, and compared to scaffolds modified using glutaraldehyde and EDC/NHS complex buffer alone. AgNP-modified scaffolds showed an improved ultrastructure, good water uptake, and considerable resistance against in vitro degradation and indentation, and a high resistance against in vitro calcification. Moreover, they were cytocompatible for allogeneic rat-BMSCs. Additionally, AgNPs did not alter the angiogenic properties of the modified scaffolds and decreased host immune responses after their subcutaneous implantation. The structural properties and biocompatibility of decellularized esophageal matrices could be improved by conjugation with AgNPs.