The intestinal absorption of lipophilic compounds such as β-carotene has been reported to increase when they are incorporated in emulsion-based delivery systems. Moreover, the reduction of emulsions particle size and the addition of biopolymers in the systems seems to play an important role in the emulsion properties but also in their behavior under gastrointestinal conditions and the absorption of the encapsulated compound in the intestine. Hence, the present study aimed to evaluate the effect of pectin addition (0%, 1%, and 2%) on the physicochemical stability of oil-in-water nanoemulsions containing β-carotene during 35 days at 4 °C, the oil digestibility and the compound bioaccessibility. The results showed that nanoemulsions presented greater stability and lower β-carotene degradation over time in comparison with coarse emulsion, which was further reduced with the addition of pectin. Moreover, nanoemulsions presented a faster digestibility irrespective of the pectin concentration used and a higher β-carotene bioaccessibility as the pectin concentration increased, being the maximum of ≈36% in nanoemulsion with 2% of pectin. These results highlight the potential of adding pectin to β-carotene nanoemulsions to enhance their functionality by efficiently preventing the compound degradation and increasing the in vitro bioaccessibility.