The Sino-German research collaboration project, “Recycling of organic residues from agricultural and municipal origin in China” (2008–2012), comprising different interdisciplinary research groups, and also German small and medium-sized enterprises, aimed at developing integrated strategies and solutions for the recycling of organic residues in China. In an intensive crop-livestock agricultural region in the Shunyi District of Beijing, five typical cropping systems were investigated. The research was conducted in the form of analyses of phosphorus (P) in soil, plants, animal feed, animal products, manures, mineral and organic fertilizers and the derivation of the corresponding nutrient balances and P flows. The mean annual P balance surplus was 492 kg·ha ·yr P for the vegetable production system, significantly higher ( <0.05) than that for orchards (130 kg·ha ·yr P) and cereal crops (83 kg·ha ·yr P). Plant-available P (Olsen-P) concentrations of topsoils (0–20 cm) had good correlations with the amounts of P applied (from mineral and organic sources). Compared to results from the Second Chinese National Soil Survey of 1981, mean concentrations of available P in soils of 19 plots investigated in Shunyi District increased 10-fold (from 7.3 to 60 mg·kg ) from 1981 to 2009. On average, the critical limit for Olsen-P concentrations (>30 mg·kg ) that can lead to increased risk of P loss was exceeded in all five cropping systems. With feed additives, the “natural background value” (Chinese Environmental Quality Standard for Soils) of copper and zinc in topsoils was exceeded at several sites. Screening for several substances in the veterinary antibiotic classes of sulfonamides, tetracyclines, and fluoroquinolones revealed widespread topsoil contamination. Calculated livestock densities were 10.6 livestock units per ha arable land in 2007. Animal husbandry is increasingly conducted in large operations, making traditional ways of reuse difficult to apply. Comparing three management systems for treatment of organic residues from a pig farm via aerobic (composting) or anaerobic (biogas) treatment in a life cycle assessment, the resulting cropland demand for a sustainable land application of biogas effluent varied between 139 and 288 ha·yr , well above the cropland area owned by the farm (10 ha). The mismatch problems in the above context between business-as-usual and improving performance are framed and discussed as (1) the mismatch between centralized animal husbandry and smallholder farming, (2) the mismatch between livestock density and cropland, (3) nutrient (including P) recycling and increasing organic matter content versus energy production, (4) subsidies for compost production and biogas, as well as (5) advances in the regulatory framework in China.