Sustainable agricultural practices have become increasingly important due to growing environmental concerns and the urgent need to mitigate the climate crisis. Digital agriculture, through advanced data analysis frameworks, holds promise for promoting these practices. Pesticides are a common tool in agricultural pest control, which are key in ensuring food security but also significantly contribute to the climate crisis. To combat this, Integrated Pest Management (IPM) stands as a climate-smart alternative. We propose a causal and explainable framework for enhancing digital agriculture, using pest management and its sustainable alternative, IPM, as a key example to highlight the contributions of causality and explainability. Despite its potential, IPM faces low adoption rates due to farmers’ skepticism about its effectiveness. To address this challenge, we introduce an advanced data analysis framework tailored to enhance IPM adoption. Our framework provides (i) robust pest population predictions across diverse environments with invariant and causal learning, (ii) explainable pest presence predictions using transparent models, (iii) actionable advice through counterfactual explanations for in-season IPM interventions, (iv) field-specific treatment effect estimations, and (v) assessments of the effectiveness of our advice using causal inference. By incorporating these features, our study illustrates the potential of causality and explainability concepts to enhance digital agriculture regarding promoting climate-smart and sustainable agricultural practices, focusing on the specific case of pest management. In this case, our framework aims to alleviate skepticism and encourage wider adoption of IPM practices among policymakers, agricultural consultants, and farmers.