Non-healing wounds are a significant problem for patients and healthcare systems worldwide. The underlying biochemistry, which drives non-healing outcomes in self-perpetuating leg wounds, is poorly understood. To address this knowledge deficit, a study of the proteins that compose the fluid, which exudates from these wounds, may provide important insight regarding treatment response and healing outcome for patients. In this respect, we have conducted a clinical study that included the collection of biological samples and clinical / psychosocial data over a 24 week period, during which time patients received best-practice care. Biological samples were analysed using both data dependent and data independent acquisition mass spectrometry to detect and quantify the protein complement of the wound fluid. The resulting data were integrated with clinical measurements and contextualized by gene ontology annotations to enable deeper insight into the dynamic biological processes taking place within non-healing wounds. This identified key biological processes that may indicate specific underlying issues for a sub-set of wounds and their recalcitrant nature towards clinical care. A suite of biological markers that are indicative of wound healing outcome were also derived from these analyses and through the use of a novel regression algorithm. Unravelling the complex biology of non-healing wounds through proteome and clinical data integration provides some insight into the mechanisms associated with a patient’s adverse or positive responses to clinical care. Such information can be developed further to inform clinical practices and enable the meaningful personalisation of wound management.