Animal manure is typically applied to meet the N needs of crops. This can lead to overapplication of P and K. We evaluated the impact of a change from N‐based applications of manure and compost without incorporation to a P‐based (crop‐removal) management system with immediate incorporation of manure on (i) silage corn (Zea mays L.) yield and quality, and (ii) soil test NO3, P (STP), and K (STK). A 5‐yr field study was conducted with annual spring applications of composted dairy solids (46 and 74 Mg ha−1), liquid dairy manure (68 and 196 kL ha−1), and inorganic N fertilizer (0 and 112 kg ha−1). Shifting from N‐ to P‐based manure and compost management reduced the corn yield by 7 to 13% and protein by 8 to 9%, suggesting that fertilizer N is needed for P‐based management. Shifting from N‐ to P‐based manure management reduced soil NO3–N at silage harvest by 39% vs. 21% for compost. After 5 yr, STP increased four‐ and sixfold and two‐ and fourfold for N‐ and P‐based manure and compost management, respectively, reflecting positive P balances (lower than anticipated yields). Soil test K increased three‐ and twofold with N‐ and P‐based manure and compost management, respectively. Both STP and STK remained unchanged with inorganic N fertilization. We conclude that a shift from N‐ to P‐based compost and manure management, with immediate incorporation of manure, leads to reduced soil P and K buildup and, for manure, also soil NO3, but supplemental inorganic N fertilization is required to ensure that crop N needs are met.