Many agricultural crops require both nitrogen (N) and phosphorus (P) fertilizers to sustain crop yields. However, long-term application of NH4–N fertilizers can cause soil acidification, which alters soil abiotic and biotic processes, including soil P dynamics. Long-term continuous wheat plots in Saskatchewan, Canada, were used to assess effects of N and P fertilization from 1967 and P fertilizer cessation in subplots from 1995. General soil chemical properties and soil P pools and forms were determined and then correlated with soil pH, total N (TN), and total P (TP) concentrations to show the relative importance on soil P dynamics of (a) crop nutrition (TN and TP); (b) soil acidification (pH); or (c) P fertilization/cessation. Fertilization with NH4–N decreased soil pH and altered exchangeable cation concentrations; however, long-term crop growth was poor in no-N plots and was best with both N and P fertilizers, in turn increasing soil carbon and organic matter. Applying P fertilizers without N increased soluble phosphates and the risk of P losses in runoff. Soil organic P (TPo) concentrations were correlated negatively to pH and positively to TN, but the concentrations of P compounds were not correlated to pH. This suggests that TPo accumulation may be from increased long-term crop residue inputs from crops with N and P fertilizers, rather than increased sorption from reduced pH. However, soil pH will continue to decrease with continued NH4–N fertilization, affecting soil chemistry and future P cycling; monitoring with a suite of wet chemistry and spectroscopic techniques is recommended.