Collagen is biocompatible, biodegradable, easy to purify, sterilize and process. It is used in many applications in drug delivery systems and tissue engineering. However, the fast biodegradation and insufficient mechanical stability necessitate stabilization of collagen via cross-linking. Tiopronin-protected gold (TIPAU) nanoclusters were used as a cross-linking agent. TIPAU form multiple amide bonds between tiopronin carboxyl groups and ϵ-amino lysine residues in collagen. Thus, the TIPAU acts as a 3D-cross-linking agent and promotes structural stability of collagen matrix. Collagen was cross-linked with various amounts of TIPAU via EDC coupling. In order to determine the degree of cross-linking and the number of bonds that can be formed between collagen molecules and a nanocrystal, TNBSA assay was employed. It was found that upon subsequent additions of TIPAU to collagen the amount of available ϵ-amino groups decreased to 0 and collagen pore size changed from 140 µm to below 1 µm. The number of cross-links that can be formed between collagen molecules and one nanocrystal was estimated to be 7.9 ± 0.5. DSC experiments demonstrate that the cross-linking of collagen with TIPAU increased its stability. The reactions of collagen mimetic peptides (Gly-Pro-Hyp)₈ containing reactive amino groups in different positions with TIPAU indicate that geometric constrains play an important role in the coupling reaction of collagen with TIPAU.