Phosphorus fertilization is essential for canola (Brassica napus) growth, but its effectiveness is influenced by environmental factors and soil characteristics. This study examined how seed-placed phosphorus affected canola emergence, biomass, yield, and root-associated microbial diversity during the 2019 and 2020 growing seasons. Higher phosphorus application rates led to reduced canola emergence and plant density, especially when placed near seeds; however, yield remained unchanged in 2020 and increased in 2019. The absence of a yield response in 2020 was likely due to elevated soil moisture and initial phosphorus levels, which improved nutrient availability regardless of fertilization. Moreover, phosphorus fertilization had a notable impact on the canola root microbiome, with a more pronounced effect in 2019 due to drier conditions. During the early vegetative stage, high phosphorus availability enhanced bacterial and fungal diversity, but this influence declined by the flowering stage, indicating a dynamic role of phosphorus in microbial selection. Additionally, canola genotypes exhibited varying phosphorus efficiency, with some maintaining better growth under phosphorus-deficient conditions. These results underscore the intricate relationship between phosphorus fertilization, environmental variability, and plant-microbe interactions, highlighting the importance of tailored fertilization strategies to maximize canola productivity.