Beyond fruit availability in rural areas, valorization into ready-to-drink beverages is limited because conventional pasteurization preserves sensory quality only with energy- and capital-intensive setups that small-scale agro-industries cannot feasibly deploy. This study designed and validated an integrated crossflow microfiltration (CFM) line tailored to rural contexts for producing high-quality beverages. The system couples crossflow microfiltration with optional in-line pasteurization of the retentate and ultra-clean bag-in-box packaging; its effects on microbial safety, composition, and process performance were evaluated across several fruit beverages. Microbial challenge tests showed >7-log reductions in aerobic mesophiles, coliforms, lactic acid bacteria, and yeasts/molds, confirming effective cold sterilization via the integrated line. Shelf life reached up to 3 months for coconut water and 5 months for blackberry juice. Hydrophilic compounds (e.g., sugars, vitamin c, anthocyanins) largely passed into the permeate, while hydrophobic compounds (e.g., carotenoids, terpenes) concentrated in the retentate; re-adding pasteurized retentate restored color and aroma. Specific energy use fell by 50–80 % versus HTST equivalent treatment, depending on processed volume and CIP cycle frequency. Overall, the validated integrated line offers a cost-effective, energy-efficient, and scalable alternative for high-quality fruit beverages, supporting sustainable rural agro-industrial development.