Diets high in vegetable consumption is highly correlated with reduced risk of developing common lifestyle related diseases. We investigated the effects of three natural growth media amendments [potassium humate, dry vermicast, volcanic minerals or Promix alone (Control)] in enhancing the accumulation of functional lipids in greenhouse grown kale. Functional lipids (n9, n6, n3 fatty acids, diglycerides, galactolipids and phytosterols) were assessed using either gas chromatography/mass spectrometry (GC/MS) or ultra-high performance liquid chromatography-high resolution tandem mass spectrometry (UHPLC-HRMS/MS). The results showed volcanic minerals and dry vermicast were the most successful in enhancing the accumulation of functional lipids in kale. For example, dry vermicast enhanced the accumulation of total C18:1n9 and C16:3n3 fatty acids, while total C18:2n6 fatty acid accumulation was enhanced by volcanic minerals. In conclusion, natural growing medium amendments are remarkably effective in modulating the accumulation of functional lipids in kale grown under controlled-environment conditions. This could be a useful strategy for functional foods production in control environment production systems. Increase access to kale with enhanced functional lipids could aid in increase consumption of these health promotive compounds in the diet with potential implications in population health.