Injection of liquid swine manure disturbs surface soil so that runoff from treated lands can transport sediment and nutrients to surface waters. We determined the effect of two manure application methods on P fate in a corn (Zea mays L.)-soybean [Glycine max (L.) Merr.] production system, with and without a winter rye (Secale cereale L.)-oat (Avena sativa L.) cover crop. Treatments included: (i) no manure; (ii) knife injection; and (iii) low-disturbance injection, each with and without the cover crop. Simulated rainfall runoff was analyzed for dissolved reactive P (DRP) and total P (TP). Rainfall was applied 8 d after manure application (early November) and again in May after emergence of the corn crop. Manure application increased soil bioavailable P in the 20- to 30-cm layer following knife injection and in the 5- to 20-cm layer following low-disturbance injection. The low-disturbance system caused less damage to the cover crop, so that P uptake was more than threefold greater. Losses of DRP were greater in both fall and spring following low-disturbance injection; however, application method had no effect on TP loads in runoff in either season. The cover crop reduced fall TP losses from plots with manure applied by either method. In spring, DRP losses were significantly higher from plots with the recently killed cover crop, but TP losses were not affected. Low-disturbance injection of swine manure into a standing cover crop can minimize plant damage and P losses in surface runoff while providing optimum P availability to a subsequent agronomic crop.