Sustainable agriculture depends on reliable phosphorus (P) supplies, yet global reserves of mineral P fertilizers are finite. Here, we explored whether organic fertilization could serve as a viable substitute for mineral P while sustaining crop yields and soil P under changing climate conditions. Using the calibrated and validated AgroC model with decades of field data from the Bad Lauchstädt long-term experiment site in Germany (with a four-crop rotation of sugar beet, spring barley, potato, and winter wheat), we simulated crop performance and soil P dynamics from 2019 to 2100 under the RCP4.5 and RCP8.5 climate scenarios. The analysis compared five fertilization strategies: mineral fertilization (MIN), two farmyard manure rates (FYM_20 and FYM_30), and two optimized manure regimes (FYM_37 and FYM_37 +N). Results showed that fertilization strategy had a far greater influence on soil P and yields than the projected climate scenarios. Low manure inputs (FYM_20) led to steady P depletion and yield loss, whereas FYM_30 and FYM_37 reduced winter wheat yield losses to 45% and 30% below MIN levels, respectively, while achieving comparable or superior yields for barley, potato, and sugar beet. Winter wheat required modest mineral N supplementation (∼15 kg N ha⁻¹) in FYM_37 +N to achieve optimal yields, while potato, barley, and sugar beet performed well under manure-only management. Warmer conditions under RCP8.5 increased P depletion by 10–15% relative to RCP4.5, but this effect remained minor compared with fertilization management. Notably, higher manure application rates were linked to lower cumulative P leaching. Among treatments, FYM_37_N performed best, with total P losses only 1.5–2% higher than those of MIN (3.77–4.82 kg P ha⁻¹ for MIN under RCP4.5 and RCP8.5). Our results suggest that optimized organic fertilization can effectively replace mineral P inputs, maintain crop yields, and enhance resilience in long-term cropping systems under climate change. • Optimized manure rates (FYM_37) sustain crop yields and soil P. • Climate effects on soil P are minor compared to fertilization strategies but increase P depletion under RCP8.5. • Additional mineral N beside organic amendment enhances winter wheat yield • Manure effectively substitutes mineral P fertilizers in long-term cropping systems.