Significance Collagens are structural extracellular matrix proteins that provide mechanical support to tissues. To gain stability, collagens can form pyridinoline cross-links via enzymatically formed intermediates initiated by lysyl hydroxylase (LH) 2. Individuals with mutations in the gene encoding LH2 share highly overlapping traits with individuals with mutations in the gene encoding the immunophilin FKBP65 that shows no LH activity. We found that FKBP65 is necessary for the dimerization of LH2, which is required for activity of LH2. Collagen cross-linking plays important roles in bone diseases as well as in such pathologies as cancer and fibrosis. Our study has elucidated a mechanism of how to interfere in a specific type of collagen cross-linking and can help advance the design of new treatments toward these pathologies.