Cover crops in sustainable agrosystems are becoming more and more applied. However, legacy effects on the growth of companion plants or following crops in rotation systems are still poorly understood, especially when Andean and ancestral crops are involved. In this work, two wheat (Triticum aestivum L.) cultivars differing in P efficiency (Kirón higher than Chevignon) were cropped together with two non-mycorrhizal plants, quinoa (Chenopodium quinoa Willd.) and amaranth (Amaranthus spp.), to study the interactions and the effects produced in the wheat rhizosphere, plant growth and mycorrhizal parameters at harvest. The plants were grown in a three-compartment plexiglass rhizobox containing an Andisol. The central compartment separated by a nylon mesh was used for the cover crops, and wheat was sown on each side. A habitual pre-crop rapeseed (Brassica napus L.), also non-mycorrhizal, was used as control. At harvest, soil (pH, available P, acid phosphatase, microbial-P), plant (phytomass, organic acid exudation, P uptake efficiency, Zn and Mn in shoots), and mycorrhizal properties (root colonization, glomalin, spore number, and hyphal density) were measured in both wheat rhizospheres. Results show that wheat cultivars differed in soil and plant characteristics affected by non-host plants being the most efficient one, better. Surprisingly, mycorrhizal propagules were not depressed, and even fungal spores with amaranth (10543 spores 100 g-1) increased 2.6-fold than control (3910 spores 100 g-1) in the P-efficient cultivar. Data obtained suggest being cautious in selecting the best wheat cultivar when using these ancestral crops, especially for wheat natives’ smallholders working in this type of soil.