Drought is a major constraint to agricultural productivity in degraded Mediterranean regions, highlighting the need for innovative strategies to sustain soil fertility and enhance crop performance. This study aimed to assess the effectiveness of an arbuscular mycorrhizal fungi (AMF) consortium, applied alone or in combination with compost (Comp), in enhancing drought tolerance in two quinoa varieties (Titicaca and Puno). To achieve this, a field trial was conducted in a completely randomized bloc design in the semi-arid region of Marrakech to evaluate plant physiological and biochemical responses, as well as changes in soil fertility, under various biofertilizer treatments (AMF, Comp, and AMF + Comp) and contrasting water regimes (well-watered (WW) vs. drought stressed (DS)). The results showed that DS reduced quinoa growth as well as physiological and biochemical parameters in both varieties. Compared to AMF and Comp, AMF + Comp improved the most quinoa tolerance to water stress under both varieties. Specifically, AMF + Comp increased grain yield by 160 and 138%, seed protein by 57 and 43%, and seed total phosphorus by 146 and 120% for Titicaca and Puno, respectively, compared to their controls under DS. Furthermore, photosynthetic activity increased whereas antioxidant enzyme activities decreased in AMF + Comp for both varieties compared to the other treatments under DS. Our results also revealed that Titicaca had a higher tolerance Index (76%) compared to Puno (54%) and a better response to biofertilizers under drought stress. Overall, these findings advance our understanding on how combining AMF and compost enhances quinoa drought tolerance under field conditions and highlight the potential use of Titicaca variety to sustain quinoa production in degraded and water-limited environments when using biofertilizers.