Although citrus processing wastewater is rich in bioactive compounds and nutrients, the significant potential of the specific feedstock for valorization still remains largely unexploited. Thus, a citrus processing wastewater-based biorefinery was employed to recover carotenoids and polyphenols, while producing microbially derived bacterial cellulose nanocrystals. The solid fraction of the effluent was applied in solid-liquid extraction using various green- and petrochemical-based solvents, yielding 1.97 ± 0.03 mg of carotenoids per g of dry solid via a mixture of D-limonene/ethanol/acetic acid. A continuous adsorption/desorption system was developed, adsorbing 89.1 ± 0.63% (w/v) of the initial phenolic content. Different solvents were assessed as elution agents maximizing the desorption of the phenolic content (76 ± 7.25%, w/v) using 75% ethanol. The remaining sugar-rich liquid was subsequently utilized for bacterial cellulose manufacture employing Komagataeibacter sucrofermentans DSM 15973. Elevated fermentative production was achieved at pH-value 6.0 using a surface-to-volume ratio of 1.53 cm⁻¹, yielding 4.98 ± 0.28 g L⁻¹ of the biopolymer following 6 d of incubation. The bacterial cellulose formed was processed using sulfuric acid, aiming to hydrolyze the amorphous fraction and produce a biomaterial of higher crystallinity as well as enhanced stability and mechanical properties as compared to the pristine biopolymer. The nanocrystals produced exhibited colloidal stability (−24.73 ± 1.11 mV), enhanced crystallinity (85.2%) and reduced thermal stability (297.1 °C) as compared to bacterial cellulose. The study demonstrated a sustainable biorefinery approach for efficient valorization of citrus processing wastewater towards production of industrially important bioactive compounds and biopolymers.