The objective of this study was to evaluate the effectiveness of a combination of UV-C disinfection treatment and a nano-coating lemon essential oil nanocapsules. The nanocapsules were prepared by ionic gelation with an alginate-pectin wall and the lemon essential oil had a particle size of 219 ± 22 nm and a zeta potential of −7.91 ± 0.18 mV. The lemon essential oil had an encapsulation efficiency of 68.19 ± 1.18%. The fresh-cut cucumber was stored for 15 days at 4 °C. Six formulations of nanocapsules were evaluated, and hydroxypropyl methylcellulose was used as matrix polysaccharide in four coatings. Three formulations were treated with UV-C at 4.5 kJ/m2. The results showed that the combination of UV-C and nano-coatings (lemon essential oil = 200 mg/L) increased the shelf life by up to 15 days. Using UV-C and nano-coatings, the ∆E value was 7.12 at the end of the storage period, while the Control samples had an ∆E of 28.1. With nano-coating treatment, the amount of polyphenols decreased by 23% within 9 days. In contrast, with combined UV-C and nano-coating treatment, the amount of polyphenols was reduced by 38.84% within 15 days. The antioxidant capacity remained stable at 459 μmol TE/100 g for the fresh product when the combined treatment was used. A good correlation was also observed between the increasing of the fruit’s shelf life and decreasing of its enzymatic activity. The inclusion of UV-C treatment contributed to the reduction in the initial total bacteria at 3.30 log CFU/g and its combination with nano-coatings helped in the control of microbial growth during storage.