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Abstract The industry standard for estimating the quantity of horticultural produce harvested is crop yield. Producing sufficient amounts of high-quality biochemical ingredients crops can therefore aid in resolving concerns with food security and nutrition. Most producers prefer the use of organic substrate over natural soils when growing crops such as peppers in greenhouses, to ensure that there is a sufficient supply of food all year round. The objective of the study was to determine the effect of coconut coir substrate on the yield and biochemical constituents of peppers varieties grown under greenhouse environment. For two successive seasons [2021 and 2022], two sweet pepper types (Sondela and Ilanga) were cultivated on fertigated coconut coir and loamy soil (control). Fruit number, together with their dry weight and some biochemical constituents, were examined. To evaluate the impact of coconut coir substrate on the growth, yield, and biochemical constituents of different pepper cultivars grown in a greenhouse, dry plant materials and freeze-dried fruit samples were analyzed. Results showed that the coconut coir and variety (Ilanga) treatment combination produced more fruits than other treatments. Biochemical constituents such as vitamins, total phenols, total flavonoids, copper, iron and Zinc were in fruits grown under coir substrate when compared to loamy soil (control). Therefore, farmers are encouraged to grow sweet peppers varieties under coconut coir substrate for better yield, nutritional quality and profit maximisation.