A polyhouse study was conducted to evaluate the relative effectiveness of different micronutrient fertilizer formulation and application methods on wheat, pea and canola, as indicated by yield response and fate of micronutrients in contrasting mineral soils. The underlying factors controlling micronutrient bioavailability in a soil-plant system were examined using chemical and spectroscopic speciation techniques. Application of Cu significantly improved grain and straw biomass yields of wheat on two of the five soils (Ukalta and Sceptre), of which the Ukalta soil was critically Cu deficient according to soil extraction with DTPA. The deficiency problem was corrected by either soil or foliar application of Cu fertilizers. There were no significant yield responses of pea to Zn fertilization on any of the five soils. For canola, soil placement of boric acid was effective in correcting the deficiency problem in Whitefox soil, while foliar application was not. Soil extractable Cu, Zn, and B concentration in post-harvest soils were increased with soil placement of fertilizers, indicating that following crops in rotation could benefit from this application method. The chemical and XANES spectroscopic speciation indicates that carbonate associated is the dominant form of Cu and Zn in prairie soils, where chemisorption to carbonates is likely the major process that determines the fate of added Cu and Zn fertilizer.