Organic fertilizers have the potential to improve soil quality and quinoa (Chenopodium quinoa Willd.) yields, but their long-standing benefits are unknown. Therefore, a three-years field experiment (2019–2022) was conducted in Morocco to investigate the residual effects of organic fertilizers on the productivity and mineral status of quinoa. Compost and manure were applied during the first season at 5, 10, and 20 t ha− 1 and 10, 20, and 40 t ha− 1, respectively. Soil organic matter (SOM), plant growth, and quinoa yield were monitored during the year of organic fertilizer applications and two and three years after the applications. 40 t ha− 1 of manure produced the highest SOM, plant height, and chlorophyll content index. Compost at 20 t ha− 1 produced the highest grain yield (4.6 t ha− 1) during the first year, but the residual effect of 40 t ha− 1 of manure exceeded other treatments in the second and third years (3.4 t ha− 1 and 1.4 t ha− 1, respectively). Average quinoa grain yield over the three years was highest with 10 and 20 t ha− 1 of compost and 20 and 40 t ha− 1 of manure and average quinoa nutrient content was 1.8 kg N, 0.3 kg P, 4.1 kg K, 0.5 kg Ca, 0.6 kg Mg, 0.5 g Cu, 1.9 g Zn, 7.9 g Mn, and 7.9 g Fe per 100 kg of total biomass. A single application of manure at 20 t ha− 1 was optimal to increase quinoa productivity for three growing seasons, promoting agricultural sustainability in arid regions.