The long-term effects of cropping practices on plant-available micronutrient concentrations in soils of the northern Great Plains of North America have not been adequately determined. We measured micronutrient uptake by wheat in a crop rotation experiment established at Lethbridge, Alberta in 1911. Phosphorus application at low rates (20 kg P ha-1 yr-1) since 1972 suppressed uptake of Zn, Cu, and Ca in the two years in which they were measured, 1991 and 1993. Vesicular-arbuscular mycorrhizal (VAM) fungi are plant symbiotic fungi that are known to increase the uptake of relatively immobile micronutrients such as Cu, P, and Zn. The functioning of these fungi is known to be affected by high-levels of P fertilization. Assessment of wheat roots showed that low-level P fertilization had significantly reduced the length of root colonized and the percentage of roots colonized by VAM fungi. The results show the importance of considering microbial ecology when assessing the effects of agricultural practices, including low-input practices, on soil productivity and crop nutrient value.