Antioxidants and flavonoids are beneficial compounds used in the pharmaceutical and food industries that are derived from natural sources. A two-year field experiment was undertaken to investigate the effect of agricultural management practices on the trigonelline content, antioxidant activity measured with DPPH (2,2-Diphenyl-1-Picrylhydrazyl) and FRAP (Fe+++-Reduction, Ferric reducing antioxidant power), total phenolic content, total flavonoids content, and specific flavonoid contents of fenugreek seeds. The treatments examined were sole fenugreek (Sole F) and three intercropping ratios with buckwheat (B) (F:B = 2:1, 1:1, and 1:2), each with three types of fertilizer (chemical fertilizer, integrated fertilizer, and broiler litter). The highest trigonelline content of fenugreek seeds was obtained in F:B = 2:1 fertilized with broiler litter. Compared to Sole F, the fenugreek seeds harvested in the intercropped treatments had higher antioxidant activity, total phenolic content, vitexin, isovitexin, orientin, and isoorientin. The treatment F:B = 2:1 enhanced the antioxidant activity and the content of bioactive compounds. Overall, the addition of organic manure to fenugreek seeds was highly effective at promoting all compounds analyzed in both the sole and the intercrop systems. Our study found that harvested fenugreek seeds from plants that were intercropped with buckwheat and with the application of organic fertilizer enhanced the seed content of antioxidants and flavonoids.