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Intercrops and organic fertilizers can improve the productivity of cropping systems due to increased soil nutrient availability and plant nutrient use efficiency. A 2-year field experiment was conducted to determine the effects of different intercropping ratios and fertilizer types on nitrogen (N) and phosphorus (P) concentrations and yields of fenugreek and buckwheat at the research farm of Shahrekord University, Iran. The treatments consisted of sole cropping of fenugreek (F), buckwheat (B) and three intercropping ratios (F:B = 1:2, 1:1 and 2:1) under three fertilizer types: chemical fertilizer (CF), integrated fertilizer (IF) and broiler litter (BL). At flowering and at harvest, intercropping increased total above-ground dry matter (TAGDM), total seed yield, N and P concentrations (plant) and uptake. The applied N use efficiency and applied N recovery efficiency (ANUE, ANRE) in the intercropped plots were also higher as compared to the sole cropping. The intercropping ratio of F:B (2:1) was the most suitable for improving the tested nutrient variables. The IF and BL showed significant benefits as compared to CF, for TAGDM, total seed yield, N-C and P-C in the plant, as well as N and P uptake in sole and intercrops. For ANUE and ANRE, CF proved to be more effective. This study showed that a 2:1 fenugreek-buckwheat intercropped system with the application of IF and BL can successfully be implemented for improving productivity, N and P contents of fenugreek and buckwheat as well as the nutrient land equivalent ratio (compared with sole cropping with CF) under semi-arid growing conditions.