Integrated crop-livestock systems (ICLS) are currently promoted agricultural production systems that aim to use better resources through production integration and intensification. While this system reduces some risks, it adds complexity and new risks to businesses due to interdependence between the agricultural modules. To deal with these issues, integrated risk management is required to reduce the effects of risks and to take advantage of the opportunities of an ICLS. Generically, enterprise risk management (ERM) meets this need by proposing comprehensive and coherent risk management, instead of managing agricultural module risks individually. However, there is a need to customize the ERM approach to ICLS. Therefore, the current study aims to develop a method to manage risks for ICLS based on ERM, integrating the management of risks and aligning risk management with the strategic objectives. A literature review, a pilot study, interviews with experts, four case studies and 20 practitioners supported the method development and evaluation through three versions. As a result, the method identifies and relates risks through process mapping with a qualitative and quantitative analysis of their impacts, determines risk responses based on willingness to take risks, and helps identify processes to control, communicate and monitor the risks. The method also stimulates the implementation of ICLS in market-oriented farms, providing an approach to increase the chances of ICLS success. The main difference from previous research lies in the integrative management of multiple risks, the alignment of risks with strategy and the consideration that a risk might be considered an opportunity.