Current tomato harvesters rely primarily on external color as the sole indicator of ripeness. However, this approach often results in premature harvesting, leading to insufficient lycopene accumulation and a suboptimal nutritional content for human consumption. Such limitations are especially critical in controlled-environment agriculture (CEA) systems, where maximizing fruit quality and nutrient density is essential for both the yield and consumer health. To address that challenge, this study introduces a novel, multimodal harvest readiness framework tailored to nutrient film technology (NFT)-based smart farms. The proposed approach integrates plant-level stress diagnostics and fruit-level phenotyping using wearable biosensors, AI-assisted computer vision, and non-invasive physiological sensing. Key physiological markers—including the volatile organic compound (VOC) methanol, phytohormones salicylic acid (SA) and indole-3-acetic acid (IAA), and nutrients nitrate and ammonium concentrations—are combined with phenomic traits such as fruit color (a*), size, chlorophyll index (rGb), and water status. The innovation lies in a four-stage decision-making pipeline that filters physiologically stressed plants before selecting ripened fruits based on internal and external quality indicators. Experimental validation across four plant conditions (control, water-stressed, light-stressed, and wounded) demonstrated the efficacy of VOC and hormone sensors in identifying optimal harvest candidates. Additionally, the integration of low-cost electrochemical ion sensors provides scalable nutrient monitoring within NFT systems. This research delivers a robust, sensor-driven framework for autonomous, data-informed harvesting decisions in smart indoor agriculture. By fusing real-time physiological feedback with AI-enhanced phenotyping, the system advances precision harvest timing, improves fruit nutritional quality, and sets the foundation for resilient, feedback-controlled farming platforms suited to meeting global food security and sustainability demands.