Integrated crop–livestock systems (ICLS) can enhance nutrient cycling and reduce dependence on external inputs, particularly in tropical Oxisols where phosphorus (P) fixation and potassium (K) mobility limit nutrient use efficiency. This study quantified annual fluxes, stocks, and balances of P and K in a soybean–pasture system under contrasting fertilization strategies, including fertilizer placement (pasture vs. soybean) and nitrogen (N) application in the pasture phase. Annual P cycling ranged from 70 to 87 kg ha⁻¹, with system fertilization increasing residual P in pasture by 18% compared to conventional fertilization. Nitrogen application enhanced soybean P uptake by 21%, although crop P balances remained positive across all treatments. Potassium cycling ranged from 178 to 198 kg ha⁻¹ and showed greater variability, with strong interactions between fertilization strategy and N supply. Potassium balances ranged from −48.9 to +18.4 kg ha⁻¹, with the largest deficit observed under system fertilization combined with N. These results indicate that fertilizer placement in pasture improves P retention and redistribution, whereas K dynamics are more sensitive to N inputs and grazing-mediated nutrient return. In tropical ICLS, short-term nutrient balances are strongly influenced by the interaction between fertilization strategy and N management, with contrasting implications for P stability and K vulnerability.