In this paper the science underpinning the Beef Profit Partnerships project methodology is explained. The science is organised around headings associated with the six key elements of the project system model which was outlined in Paper 1 and is described in more detail in Paper 4. The headings are: (1) Focus, targets, outcomes and key measures; (2)Partnerships, networks, social infrastructure and social capital; (3) Technology and information – development, integration, valuation and diffusion; (4) Continuous improvement and innovation process and tools; (5) Capacity, tools and expertise; and (6) Momentum, culture development and institutionalisation.