In order to study the effects of biological nutrition and irrigation managements on qualitative indices of fenugreek, an experiment was carried out in split plot based on a Randomized Complete Block Design with three replications and 15 treatments at Research Station, Faculty of Agriculture, Azad University, Birjand, Iran, during growing season of 2010-2011. Experimental treatments included irrigation interval (in three levels including irrigation every 6, 9 and 12 days) and biofertilizer (in five levels including nitroxin, biosphere, and micorhyza fungi of G. mosseae, G. intraradices and control treatment or none fertilizer). Results of statistical analysis showed that irrigation treatments had a significant effect on physiological indices like carbohydrate, chlorophyll a, ash, Na, K and proline. The effect of biofertilizer was significant on carbohydrate, chlorophyll a, and on ash. Results showed that proline, carbohydrate, Na, chlorophyll b and ash improved by increasing irrigation interval to every 12 days but K and chlorophyll a decreased. The highest content of carbohydrate, chlorophyll and ashwere observed in G. mosseae, biosphere and G. intraradices, respectively. Overall, results showed that application of biofertilizers had positive effects on qualitative indices of fenugreek and created type of plant adaptation to drought stress.