An appropriate fertilization strategy is essential for improving micronutrient supply, crop nutrition, yield and quality. Comparative effects of different application strategies of micronutrient fertilizer were evaluated in two contrasting sites/soils (upper slope Chernozem and lower slope Solonetz) within a farm field located in the Brown soil zone of Saskatchewan, Canada. The study objective was to examine the impact of Cu, Zn, and B fertilizer application strategies on their mobility, bioavailability and fate in the soil as well as crop yield responses. The application strategies were broadcast, broadcast and incorporation, seed row banding, and foliar application of Cu, Zn, and B on wheat, pea, and canola, respectively. The study was laid out in a randomized complete block design (RCBD) with four treatment replicates for a specific crop and site. Crop biomass yields were not significantly influenced by micronutrient placement strategies at both sites. Pea tissue Zn concentration (35.2 mg Zn kg−1 grain and 5.15 mg Zn kg−1 straw) was increased by broadcast and incorporation of Zn sulfate on the Solonetz soil. Residual levels of soil extractable available Cu were increased significantly to 3.18 mg Cu kg−1 soil at Chernozem and 2.53 mg Cu kg−1 soil Solonetz site with the seed row banding of Cu sulfate. The PRS™-probe supply of Cu (1.84 µm Cu/cm2) and Zn (1.18 µm Zn/cm2) were significantly higher with broadcast application of corresponding micronutrient fertilizer in the Chernozem soil. Both the chemical and spectroscopic speciation revealed that carbonate associated Cu and Zn were dominant species that are likely to control the bioavailability of these micronutrients under field conditions.