Melanins are conjugated biopolymers with varying compositions and functions, found in various tissues throughout the body. Here, the conjugated polymers derived from homogentisic acid (HGA), polyHGA (a simplified model of pyomelanin), formed in an ex vivo tendon model are examined with a view to understanding interactions between melanins and the extracellular matrix (ECM) using a selection of different analytical techniques, including spectroscopy (energy dispersive X‐ray, infrared, and Raman), X‐ray diffraction, and microscopy (electron, optical, and scanning electrochemical). The combination of techniques was used to facilitate an understanding of subtle differences in the composition and distribution of ECM components, hydroxyapatite, and melanin in the tendons for the first time. PolyHGA deposition in connective tissues in patients with alkaptonuria is a significant burden and causes multiple tendon ruptures due to the significant alterations in collagen properties. A similar pathology is seen in the wider population from calcific tendinitis because of hydroxyapatite crystal deposition in tendons of the shoulder and lower limbs, in particular.