Escalating pathogen resistance to synthetic pesticides and the regulatory impetus of the European “Farm-to-Fork” Strategy have intensified the search for crop-protection tools that eliminate toxic residues while safeguarding yield. In this context, we investigated the antifungal potential of five plant-derived extracts—Azadirachta indica (neem), Salix babylonica (willow), Capsicum annuum (chilli), Thymus vulgaris (thyme), and Allium sativum (garlic)—against the economically important tomato pathogens Phytophthora infestans, Alternaria solani, and Botrytis cinerea. Crude extracts were produced by ultrasound-assisted extraction in 70% (v/v) ethanol, achieving mean yields of 12–18% (w/w) relative to dry biomass. Each extract was encapsulated in chitosan–alginate nanoparticles (mean diameter 145 ± 18 nm; ζ-potential –31 mV) to enhance stability and foliar adhesion. Formulations were sprayed at 0.5–2 g L⁻¹ in a 10-week greenhouse trial (1 000 m², completely randomized design, three replicates per treatment). In vitro disc diffusion assays confirmed dose-dependent growth inhibition, with minimum inhibitory concentrations ranging from 0.25 to 1.0 g L⁻¹. In vivo, the T. vulgaris nanoformulation curtailed disease incidence by 67%, statistically indistinguishable from the synthetic fungicide fludioxonil (p > 0.05), yet left no quantifiable residues in fruit (< 0.01 mg kg⁻¹ by LC-MS/MS). A cradle-to-gate life-cycle assessment, performed according to ISO 14040/44, revealed that the thyme-based treatment reduced eutrophication potential by 55% and greenhouse gas emissions by 40% relative to the grower’s conventional spray program. Sensitivity analysis indicated that nanoparticle encapsulation contributed less than 5% to the overall impact, validating its environmental compatibility. Our findings demonstrate that nano-carried botanical extracts can match the efficacy of commercial fungicides while advancing zero-pollution objectives. The approach offers a scalable pathway for integrating circular bio-resources into plant-health management and supports EU policy goals for pesticide-free, climate-smart agriculture.