One of the most important factors that limits crop production is the availability of water. Deficit irrigation is the most important irrigation strategy to increase water use efficiency and crop water productivity. Organic amendment combined with deficit irrigation can be practical solution to compensate the negative effect of water deficit through the improvement of soil water-holding capacity. This research was conducted in the south of Morocco (IAV-CHA, Agadir) between October 2011 and January 2012. The mean objective of this study was to evaluate the combined effect of organic matter and deficit irrigation with treated wastewater on quinoa (Chenopodium quinoa Willd.) productivity. Three organic matter levels (0, 5, and 10 t ha−1) have been supplied as compost amendment combined with two deficit irrigation levels (50 and 100% of full irrigation). Statistical analysis revealed very highly significant difference only between deficit irrigation treatments for most measured parameters. However, significant difference was obtained between organic matter treatments in terms of grain yield. The highest grain yield (66.3 g plant−1) has been recorded when quinoa was subjected to full irrigation and received 10 t ha−1 of compost; however, the lowest yields were obtained by treatments receiving 50% of full irrigation without organic matter supply. From the findings, it can be concluded that reducing irrigation requirement by half affected negatively quinoa growth and productivity and reduced grain yield by 36%, organic amendment improved significantly yield and biomass production better under deficit irrigation conditions.