Hides and skin preservation has been prominently undergoing salt curing technique for centuries which uses high amount of NaCl (40%) that causes huge amount of total dissolved solids (TDS) and salinity in soaking wastewater of leather processing. Recently, Phyto based preservation is getting emphasis due to being sustainable with less environmental impact. In this study, Gossypium hirstum (cotton) seed powder (5%-7.5%) with 10% salt were applied as a novel source for goatskin preservation. Curing efficiency was monitored by checking organoleptic property, physiochemical property (moisture content, shrinkage temperature, bacterial count, nitrogen content, etc.) at regular interval. Accomplishing the preservation period, preserved skins were processed into shoe upper leather. The pollution parameters were checked from soaking waste liquor to evaluate the environmental impact. SEM analysis and physical properties of the were evaluated to the quality of the produced shoe upper leather. The results revealed that newly developed preservative can preserve goatskin up to 28 days without any deterioration. Experiments reduced pollution by lowering chloride levels 65.33%-66.91%, total dissolved solids by 41.06%-35.2%, biochemical oxygen demand by 30.86%-34.28% percent, and chemical oxygen demand by 41.06%-35.2%. According to the correlation study, there were significant dependencies between the goatskin preservation efficacy parameters, with various strong correlation (r = − 0.976, p<0.001) found between shrinkage temperature and moisture content. Surface topography, physical strength of the produced leather was compatible to conventional shoe upper leather. Thus the introduced seed powder could be one of the valuable sources of eco-friendly leather preservation to reduce environmental pollution.