Nanoemulsions have been widely studied as lipophilic compound loading systems. A low-energy emulsification method, phase inversion composition (PIC), was used to prepare oil-in-water nanoemulsions in a carvacrol–coconut oil/Tween 80®–(linoleic acid–potassium linoleate)/water system. The phase behaviour of several emulsification paths was studied and related to the composition range in which small-sized stable nanoemulsions could be obtained. An experimental design was carried out to determine the best formulation in terms of size and stability. Nanoemulsions with a very small mean droplet diameter (16–20 nm) were obtained and successfully encapsulated to add carvacrol to foods as a natural antimicrobial and antioxidant agent. They were encapsulated into alginate beads by external gelation. In order to improve the carvacrol kinetics release, the beads were coated with two different biopolymers: chitosan and pullulan. All formulations were analysed with scanning electron microscopy to investigate the surface morphology. The release patterns at different pHs were evaluated. Different kinetics release models were fitted in order to study the release mechanisms affecting each formulation. Chitosan-coated beads avoided the initial release burst effect, improving the beads’ structure and producing a Fickian release. At basic pH, the chitosan-coated beads collapsed and the pullulan-coated beads moderately improved the release pattern of the alginate beads. For acid and neutral pHs, the chitosan-coated beads presented more sustained release patterns.