The citrus red mite, Panonychus citri (McGregor) (Acari: Tetranychidae), is a major pest of citrus crops, often managed through repeated applications of plant protection products. Intensive pesticide use can lead to resistance in pest populations and negatively affect beneficial organisms. The predatory mite Euseius stipulatus Athias- Henriot (Acari: Phytoseiidae) is a key natural enemy and a crucial component of integrated pest management (IPM) programs. This study aimed to assess resistance in P. citri populations from citrus-growing regions of Greece using combined phenotypic and molecular approaches and to evaluate the side effects of widely used plant protection products on E. stipulatus. P. citri populations were collected and tested in single-dose toxicity bioassays at recommended field rates of abamectin, acequinocyl, cyflumetofen, fenpyroximate, pyridaben, spirotetramat, and hexythiazox. The same products were evaluated on E. stipulatus under laboratory bioassays. Four green-technology products— Eradicoat, Pre-Vam, Requiem, and Flipper—were tested in both species. Resistance mechanisms in P. citri were assessed using droplet digital PCR (ddPCR) assays targeting validated mutations (H110R, F1538I, I1017F, G126S/ A133T, F752C). Most P. citripopulations were sensitive to the tested substances, with low or absent resistance mutations. One population exhibited multi-formulation resistance with high-frequency target-site mutations, highlighting H110R and G126S/A133T as predictive biomarkers. Abamectin, spirotetramat, and pyridaben caused very high mortality (>93%) in E. stipulatus, whereas acequinocyl, acetamiprid, cyflumetofen, fenpyroximate, and hexythiazox showed minimal toxicity (<11%). Green-technology products displayed variable effects on E. stipulatus (low: Requiem 20%; moderate: Eradicoat 48%; high: Pre-Vam 71%; Flipper 98%) and high efficacy against P. citri (80–100% mortality) in both resistant and susceptible populations. These findings demonstrate that integrating pest resistance monitoring with the selection of predator-compatible plant protection products is essential for effective IPM. Tailoring pesticide use to target pest susceptibility while conserving beneficial arthropods enhances biological control and supports the long-term sustainability of citrus production systems Acknowledgments: This work was supported by the National Recovery and Resilience Plan Greece 2.0 with the funding of the European Union – InnoPP- TAEDR-0535675 and received funding from the European Union’s HORIZON-IA (101136611 -NextGenBioPest).