Wound healing is a complex multi-step process that requires the conjoint activity of numerous molecular and cellular pathways. Classically in the adult it is initiated by an inflammatory phase that drives endothelial, fibroblast and keratinocyte proliferation to be followed by scarring. In parallel, the breach in cutaneous barrier is also a unique scenario where the skin microbiota is in direct contact with the immune system. Many studies have envisioned a segmented approach to wound healing considering only one system or one molecule at a time. We have conducted a genome wide association study identifying quantitative trait loci for wound closure across 70 strains of mice and within 40 of these strains we have characterised in more detail the scarring and microbial colonization. This provides for the first time a unique perspective on the complexity of wound healing in an unbiased multi-omics approach creating hope for an era of targeted therapy in skin wound care.