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BACKGROUND: Genetic improvement of crop varieties requires significant investment. Therefore, varieties must be developed to suit a broad range of breeding targets, such as yield and suitability to rainfall zones, farm management practices and quality traits. In the case of breeding for disease resistance, breeders need to consider the value of genetic improvement relative to other disease management strategies and the dynamics of pathogen genetic and phenotypic diversity. This study uses a benefit–cost analysis framework to assess the economic value of fungicide management and crop genetic improvement in disease resistance for Australian chickpea varieties. RESULTS: When assessing the likelihood of growers switching to new crop varieties with improved genetic resistance to disease, the simulation results reveal that adopting these varieties yielded higher net benefit values compared to implementing current fungicide strategies across all rainfall zones. On average, the increase in net benefit varied between 2.6% and 3.5%. Conversely, when we examined the scenario involving modifying the current fungicide strategy, we observed that, on average, switching from the current fungicide management strategy to one which involved additional fungicides was beneficial in about 73% of the cases. CONCLUSION: Our analysis reveals the importance of factors such as commodity prices, production costs, disease‐related variables and risk aversion in determining the economic benefits of adopting new crop protection strategies. Furthermore, the research reveals the need for accessible information and reliable data sources when evaluating the benefits of new agricultural technologies. This would assist growers in making informed and sustainable disease management decisions. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. [ABSTRACT FROM AUTHOR]