The increasing demand for safe, sustainable, and effective food preservation strategies has stimulated interest in technologies capable of overcoming the limitations of conventional preservation approaches. Essential oil nanoformulations (EONFs) have emerged as promising preservation platforms because they improve the stability, bioavailability, and controlled release of essential oils (EOs) while reducing volatility, degradation, and sensory impacts. Simultaneously, advances in artificial intelligence (AI) and foodomics are creating new opportunities for developing predictive and mechanistically informed preservation systems. This review critically examined recent progress in EONF technologies, including nanoemulsions, lipid-based nanocarriers, mesoporous delivery systems, and biopolymeric encapsulation platforms, with emphasis on their antimicrobial mechanisms, release behavior, and food applications. The review further evaluates how AI-driven approaches can support formulation optimization, spoilage prediction, shelf-life modeling, and smart packaging applications through integration of sensor-derived and environmental datasets. In parallel, foodomics technologies, encompassing transcriptomics, proteomics, metabolomics, and lipidomics, are discussed as powerful tools for elucidating EO–microbe–food interactions and identifying molecular biomarkers relevant to preservation efficacy. Particular attention is given to the integration of EONFs, AI, and foodomics within a unified framework that links mechanistic understanding with predictive decision-making. The review also critically discusses key barriers to implementation, including formulation scalability, compositional variability of EOs, omics-data latency, data heterogeneity, AI interpretability, regulatory uncertainty, and economic feasibility. Rather than proposing a new preservation technology, this work provides a translational roadmap for integrating responsive nanoformulations, foodomics-derived biomarkers, smart sensing platforms, and AI-enabled analytics into adaptive preservation systems. Such an approach may facilitate more precise, evidence-driven, and sustainable food preservation while supporting improvements in food safety, shelf-life management, and waste reduction across modern food supply chains.