Quinoa cultivation is well-adapted to sustainable cropping systems, even if seed yield could be severely limited due to several constraints, such as weeds. Field trials were performed in Gorgan (Iran) to quantify the effects of agro-ecological service crops (rye, CCr; winter vetch, CCw; and no cover, CC0), tillage regimes (conventional tillage, CT; and no-tillage, ZT), and herbicide rates (100% rate, H100; 75% rate, H75; and without herbicide, H0). Weed characteristics and quinoa yield were measured. Quinoa seed yield was the highest in CCw-ZT-H100. Seed yield in H100 and H75 were higher compared with H0 (2.30 vs. 1.58 t ha−1, respectively). Under conventional tillage, 46% of weed seeds were observed in the 0–10 cm soil layer and 54% in 10–20 cm soil layers, respectively, while, under no-tillage, about 63% of weed seeds were located up to 10 cm of soil. Amaranthus retroflexus L. was the most abundant species. The total weed density was the lowest in CCr-ZT-H100 and tended to be higher in CC0 (30.9 plant m−2) and under CT (29.0 plant m−2). These findings indicate that cover crops have potential for managing weeds in quinoa; however, their inclusion should be supported by chemical means to maintain high seed.