Downstream from the wastewater treatment plant (WWTP), reaching 1437 mg·l⁻¹. For the nitrites, a level exceeding the limits, especially upstream, had an average of 2.03 mg·l⁻¹ and a maximum of 5.48 mg·l⁻¹. Upon studying the soil samples, a substantial emphasis was placed on the urgent need to carefully manage this treatment, combined with the reasonable use of agrochemical inputs to prevent their leaching into nearby ecosystems. By doing so, we can effectively reduce the risks to both the ecosystem and human health in the study region. Due to drought and low soil fertility, Moroccan farmers have a limited choice of crops. In this context, quinoa (Chenopodium quinoa) is considered a promising alternative due to its adaptability to arid and semi-arid conditions. This study investigated the effect of fertilising quinoa with four digestates derived from the anaerobic co-digestion of olive mill wastewater (OMW), with fruits and vegetable waste [FVW], fish waste [FW], and cow dung [CD]. In addition, the combined effects of these digestates with chemical fertiliser were evaluated. The experiment was conducted under greenhouse conditions to evaluate the effects on the agronomic, morphological, and physiological parameters of quinoa. The results showed that the highest grain yield (16 q·ha⁻¹) was obtained with the treatment [CD-Mx]R2:1-NPK, followed by [CD-OMW]R3:1-NPK (14 q·ha⁻¹), whereas both the negative and positive controls produced 13 q·ha⁻¹. The effects on morphological and physiological parameters, such as plant height, number of leaves, leaf area, number of inflorescences, chlorophyll content, and the ‘1000 seed’ weight, were quite disparate and significantly differed among all treatments.