Growing pea in rotation with wheat is expected to modify soil microbial community structure and functionality. This was tested in a ten year long-term experiment located in a Black Chernozem of Saskatchewan. The experiment included: three N rates; 0, 20 and 40 kg N ha^-1 applied to each crop in rotation and two crop rotations: pea after pea (pea-pea) and pea after wheat (wheat-pea). Soil (0-7.5 cm) and plant were sampled three times during the pea crop season. Nitrogen application did not influence soil and plant parameters except decreased AM fungal root colonization. Pea biomass was higher in wheat-pea than pea- pea and the differences widened with crop growth. Lower soil NO₃ flux in wheat-pea than pea-pea corresponded to more N uptake by pea after wheat. Soil PO₄ flux did not vary with cropping systems and the increase in plant P content in wheat-pea could be attributed to increased AM fungal root length colonization. Increase in soil dehydrogenase, phosphatase and urease activities in wheat-pea could have resulted in increased mineralization and subsequent uptake of N, P and K by pea thereby improving pea biomass. The increase in specific microbial activity in wheat-pea indicated higher nutrient cycling in this phase. Cropping system significantly, influenced soil microbial community structure (PLFA profile) as determined by backward stepwise discriminant analysis with no effect of N fertilization. We conclude that long-term N fertilization reduced AM fungal root colonization but growing pea and wheat in rotation increased pea biomass by improving AM fungal development and modifying microbial community structure and functionality.