Supplying organic matter under deficit irrigation conditions could be a practical solution to compensate the negative effect of water stress. For this purpose, studies in pea as a legume and quinoa as a new drought‐tolerant crop were conducted in the south of Morocco between October 2011 and March 2012. Three organic matter levels (0, 5 and 10 t ha⁻¹) were supplied as compost amendment combined with 2 irrigation levels (50 and 100% of full irrigation). The results indicate that stomatal conductance and dry matter have been affected significantly (P < 0.05) only by deficit irrigation, while harvested yield was affected significantly (P < 0.05) by both deficit irrigation and organic manure. The highest seed yields (3.3 t ha⁻¹ for quinoa and 5.6 t ha⁻¹ for pea) were recorded under full irrigation and 10 t ha⁻¹ of compost. Results indicated that organic amendment of 10 t ha⁻¹ and 5 t ha⁻¹ significantly (P ≤ 0.05) increased seed yield by 18 and 11% under stress conditions and by 13 and 3% under full irrigation for quinoa and by 24 and 11% under full irrigation and by 41 and 25% under water‐deficit irrigation for pea. It can be concluded that organic amendment improved significantly yield and biomass production better under deficit irrigation conditions than under full irrigation. Combining deficit irrigation and organic amendment led to the maximization of crop water productivity.