Production of arable crops in Switzerland is subsidized for services performed within the Proof of Ecological Performance (PEP) program, the crop protection part of which is based on IPM principles. Within PEP, chemical insect control must rely on those approved insecticides that are deemed harmless for beneficial arthropods. Approved insecticides potentially impacting beneficial arthropods may also be applied, but only if unavoidable and with an official permit. In order to assess the ecological and economic sustainability of this PEP program, a reference insecticide strategy illustrating the current PEP requirements was compared with other strategies. For this purpose, a sustainability assessment taking account of ecotoxicological risks and economic viability in addition to the preservation of beneficial arthropods was performed according to the SustainOS methodology. The results show that the one-off use of Audienz (spinosad) to control cereal leaf beetle (Oulema melanopus)—a key pest in winter wheat—would significantly improve sustainability vis-à-vis the reference (Nomolt (teflubenzuron) plus Biscaya (thiacloprid)). However, in the case of the Colorado potato beetle (Leptinotarsa decemlineata), in potato crops, where Audienz is considered the reference, no alternative would exhibit better sustainability. Moreover, the study shows that strategies using Novodor (Bacillus thuringiensis) protect beneficial species well but have the drawbacks of increased yield risk and higher costs. The conclusions drawn from these analyses allow recommendations for modifications of the PEP requirements for these two pest insects. The SustainOS methodology, a multi-step process combining expert knowledge with quantitative assessments including a sensitivity analysis of key target parameters and a rule-based aggregation of assessment results, yielded valuable insights into the sustainability of different crop protection strategies.