The use of natural inputs can be an eco-friendly strategy to improve the quantitative and qualitative characteristics of plants in sustainable agriculture. This experiment aimed to compare the yield, nutrients, secondary metabolites, and fatty acids of borage and peanut affected by organic fertilizer versus chemical fertilizers in an intercropping system. The experiment was conducted in a factorial arrangament using a randomized complete block design with three replications during two consecutive years, 2021 and 2022. The experimental factors included the cropping pattern in four ratios (sole cropping of borage and peanut, 50% additive intercropping of borage and peanut, and 100% additive intercropping of borage/peanut) and fertilizers at three levels (control, organic, and chemical fertilizer). The organic fertilizer (24 t ha− 1) consisted of digested organic matter prepared by anaerobic fermentation of food wastes and cow manure. The chemical fertilizers included urea and triple superphosphate (140, and 100 kg ha− 1, respectively). The results showed that the 100% intercropping treated with organic fertilizer increased the anthocyanin, tannin, phenol, and mucilage values by 4.7%, 7.8%, 12.5%, and 7.7%, respectively, compared to those with chemical fertilizer. The maximum NPK uptake in borage was observed in intercropping patterns, while in peanuts, it came from sole cropping. The intercropping patterns treated with organic fertilizer reduced the stearic and palmitic acid content of borage by 64.2% and 49.6%, respectively, compared to the control. Finally, it is recommended that farmers use this organic fertilizer to produce borage in the intercropping system with peanut.
