Crop protection in general and apple crop protection in particular often rely on pesticides, although several alternative pest management measures are available. In this context European agricultural policy requires the implementation of Integrated Pest Management (IPM) by 2014. Within IPM, more than one strategy can be practiced but selecting the most sustainable strategy is difficult because it requires simultaneous assessment of multiple environmental and economic aspects or attributes. Here, we introduce the SustainOS methodology for sustainability assessment of orchard systems, and we evaluate its usefulness in a case study involving four crop protection strategies in apple orchards of five European regions. SustainOS is an iterative, multi-attribute approach for defining and rating the sustainability of crop protection strategies in comparative studies. It consists of a transparent system-description tool including context, target, and crop protection parameters. The parameters are used as input data for life cycle assessment, environmental risk assessment, and full-cost calculations. The various results from these quantitative assessments are used to generate a multi-attribute rating with respect to ecological and economic sustainability. We demonstrate how the quantitative results can be translated into rating classes. By applying the SustainOS methodology, we show that the ecological sustainability for all five regions can potentially be improved by implementing alternative crop protection measures currently available. We also report that, by increasing yield, yield stability, and fruit quality, implementation of IPM can improve the economic situation of apple growers. Because of its transparency, SustainOS facilitated the collaborative development and comparison of crop protection strategies for sustainable orchard systems by an international network of agronomists, economists, and environmental scientists.