Continuous manure application based on crop nitrogen (N) requirements could substantially increase field nutrient losses from croplands. Although phosphorus-based (P) manure application is an alternative, crops may suffer from potential microbial P immobilization and fixation of P in soil. A three-year study (2012–2014) was carried out in Manitoba, Canada, to evaluate the agronomic and environmental benefits and tradeoffs between N- and P-based liquid and solid swine manure applications on previously established (2009) annual (ACS) and perennial (PCS) cropping systems. The N-based solid manure produced greater aboveground biomass and grain yields of barley than the unfertilized control in the ACS. The N-based liquid manure produced greater biomass than the control in the PCS. Phosphorus-based treatments produced statistically similar canola oilseed grains as the N-based treatments. Seeding the PCS to canola in 2013 produced greater aboveground biomass yields than the ACS; however, the canola oilseed yields were not significantly different between the two systems. The N-based solid manure application increased Olsen P by approximately 30 mg kg−1 in both cropping systems during the three-year study period. Both N- and P-based liquid manure treatments and the N-based solid manure treatment lost significantly greater nitrate through leaching than the control in 2013, when most leaching losses occurred. Our study also showed that some of the environmental benefits of the perennial cropping system, such as reduced nitrate leaching, could be lost when converted to an annual cropping system.