Management of animal manure in livestock and crop production is a major cause of nitrogen (N), phosphorus (P), and carbon (C) loss. The losses of N, P, and C contribute to adverse environmental impacts, such as climate change, terrestrial acidification, and marine eutrophication. Manure management technologies to reduce losses and impacts have been developed, but often focus on a single compound only or a single stage in the management system and lead to trade-offs, such as pollution swapping. The aim of this study was to design strategies for integrated manure management (IS) which prevent pollution swapping and show that the environmental impact can be reduced throughout the manure management system. We used a structured design approach based on engineering design (ED) that consists of eight main steps: 1. define the goal of the design task and the system boundaries, 2. formulate a brief of requirements stating the needs for environmental reduction, 3. analyze the functions in the current manure management system, 4. list and describe emission processes and their process variables that lead to N, P, and C losses and resource use, 5. describe the functions needed in the manure management system to limit the emission processes or resource use, 6. generate principle-options that can fulfill the functions, 7. generate technical solutions for the principle-options, and 8. combine the principle-options and technical solutions into strategies for integrated manure management. In the design of strategies we considered the management of liquid and solid dairy cattle manure applied to grass and maize, and liquid pig manure applied to wheat, all under North West European conditions. The IS included the segregation of pig and dairy cattle urine and feces to reduce CH4, NH3, and N2O emission, addition of zeolite to solid cattle manure to reduce NH3 emission, bio-energy production from biogas that avoids fossil-based electricity and heat, acidification of urine during storage and acidification of feces prior to application, sealed storages, and improved application timing, place, and method of application. It was concluded that we were able to successfully design IS with high potential to reduce environmental impact. The design approach adapted from ED proved to be useful to structure the design process to provide insight into interactions of emission processes and find principle-options and technical solutions to prevent pollution swapping.