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Abstract Phosphorus (P) budgets for cropping systems provide insights for keeping soil P at optimal levels for crops while avoiding excess inputs. We quantified 12 years of P inputs (fertilizer and atmospheric deposition) and outputs (harvest and leaching losses) for replicated maize (Zea maysL.)—soybean (Glycine maxL.)—wheat (Triticum aestivum) crop rotations under conventional, no‐till, reduced input, and biologically based (organic without compost or manure) management systems at the Kellogg Biological Station LTAR site in southwest Michigan. Conventional, no‐till, and reduced input systems were fertilized between 13 and 50 kg P ha⁻¹depending on year. Soil test phosphorus (STP) was measured at 0‐ to 25‐cm depth every autumn. Leached P was measured as dissolved P in the soil solution sampled beneath the rooting depth and combined with modeled percolation. Fertilization and harvest were the predominant P fluxes in the fertilized systems, whereas only harvest dominated P flux in the unfertilized organic system. Leaching losses were minor terms in the budgets, but leachate concentrations were nevertheless close to the range of concern for downstream eutrophication. Over the 12‐year study period, the organic system exhibited a negative P balance (−82.0 kg P ha⁻¹), coinciding with suboptimal STP levels, suggesting a need for P supplementation. In contrast, the fertilized systems showed positive P balances (mean: 70.1 kg P ha⁻¹) with STP levels well above agronomic optima. Results underscore the importance of tailored P management strategies to sustain crop productivity while mitigating environmental impacts.