This manual presents the second version of the EU-wide individual farm level model IFM-CAP which has been developed to assess the economics and environmental impacts of the CAP and related policies, such as the Strategies embedded in the European Green Deal. The rationale for such a farm-level model is based on the increasing demand for a micro simulation tool capable to model farm-specific policies and to capture farm heterogeneity across the EU in terms of policy representation and impacts. Based on Positive Mathematical Programming, IFM-CAP seeks to improve the quality of policy assessment upon existing aggregate and aggregated farm-group models and to provide assessment of distributional effects over the EU farm population. To guarantee the highest representativeness of the EU agricultural sector, the model is applied to every EU-FADN (Farm Accountancy Data Network) individual farm (83,292 farms). The present manual provides a detailed description the IFM-CAP model (IFM-CAP V.2) in terms of design, mathematical structure, data preparation, modelling livestock activities, allocation of input costs, modelling of the current CAP setting (2013-2020) and calibration process. The theoretical background, the technical specification and the outputs that can be generated from this model are also briefly presented and discussed.