This research provides an analytical and predictive framework, based on state-of-the-art machine-learning (ML) algorithms (random forest (RF) and generalized additive models (GAM)), that can be used to assess and improve the Common Agricultural Policy (CAP) impact/performance over the agricultural and rural environments, easing the identification of proper instruments that can be used by EU policy makers in CAP’s financial management. The applied methodology consists of elaborating a custom-developed analytical framework based on a dataset containing 22 relevant indicators, considering four main dimensions that describe the intricacies of the EU agricultural and rural environment, in the CAP context: rural, emissions, macroeconomic, and financial. The results highlight that an increase of the agricultural research and development funding, as well as the agriculture employment rate, negatively influence the degree of rural poverty. The rural GDP per capita is influenced by the size of the employment rate in agriculture. It seems that environmental sustainability, identified by both fertilizers used and emissions from agriculture parameters, significantly influences the GDP per capita. In predicting emissions in agriculture, the direct payment, degree of rural poverty, fertilizer use, employment in agriculture, and agriculture labor productivity are the main independent parameters with the highest future importance. It was found that when predicting direct payments, the rural employment rate, employment in agriculture, and gross value added must be considered the most. The agricultural, entrepreneurial income prediction is mainly influenced by the total factor productivity, while agricultural research and development investments depend on gross value added, direct payments, and gross value added in the agricultural sector. Future research, related to prediction models based on CAP indicators, should also consider the marketing dimension. It is recommended for direct payments to be used to invest in upgrading the fertilizers technologies, since environmental sustainability will influence economic growth.