Food safety is a critical public health issue requiring a shift from reactive crisis management to proactive, predictive governance. This study introduces an end-to-end deep learning framework, built upon a recurrent neural network architecture, to forecast monthly dairy-related food safety notifications from the EU’s Rapid Alert System for Food and Feed (RASFF). By integrating a diverse set of economic, environmental, social, and technological indicators from five EU countries (2001–2024), the model provides explicit, forward-looking risk predictions. The framework’s core innovations include a robust in-model strategy for handling missing data, which avoids traditional imputation bias, and an interpretability method that reveals the direction and temporal scale of risk drivers. The model achieved strong predictive performance, strategically prioritizing public health sensitivity with a high recall of 80.34%, a balanced F1-score of 71.21%, and an AUC-ROC of 0.8292. The interpretability analysis revealed that systemic risk is driven by a composite of factors with distinct temporal signatures: chronic, year-round pressures (e.g., antibiotic usage), seasonal risks (e.g., temperature), and long-lagged structural influences (e.g., agricultural income). By unifying forecasting with multi-level interpretation, this research provides a validated blueprint for intelligent early warning systems. It offers actionable, temporally-specific insights that enable policymakers, industry, and researchers to advance a more agile and data-informed approach to food safety.