In order to effectively conserve the non-renewable resource phosphorus (P), flows and stocks of P must be known at national, regional and global scales. P is a key non-renewable resource because its use as fertilizer cannot be substituted posing a constraint on the global food production in the long-term. This paper presents a methodology to establish country-wide P balances that emphasises resource use. We develop a material flow analysis (MFA) model that comprises all relevant flows and stocks of P in five subsystems, seven processes and 36 material flows. For quantification, statistical data from economic and agricultural sources as well as available information about P partitioning in natural and anthropogenic processes are used. Special attention is paid to data gaps and uncertainties. The model was tested in two case studies on P management in Turkey and Austria. MFA appears to be a tool well suited for establishing country-wide P balances, provided that national statistics are well-structured and accessible. If a common approach is used for modelling P-flows and stocks, regional and national balances can be compared and linked towards larger scale P balances for an improved management of the resource.