Chemical disinfectants along with various mechanical methods are still commonly used in the food industry to disinfect food contact surfaces. A new strategy that could replace them is by encapsulating carvacrol (CAR) and thymol (THY) in monolayer (ML) and layer-by-layer (LBL) nanocapsules. ML nanocapsules were developed using a single carrier material maltodextrin, whereas pectin was additionally added to the LBL nanocapsules. Physicochemical characterizations (size, charge, polydispersity index) and microscopy observations of nanocapsules revealed increased size and thickness of the wall shell with the additional layer in the LBL nanocapsules. The release kinetics of CAR and THY over a 20 h period fitted into the Korsmeyer-Peppas model and followed a Fickian release behavior combining dissolution and diffusion. ML nanocapsules revealed an initial burst release of terpenes with 90.52% released during the first 2 h, followed by a steady release phase. Whereas, only up to 50.71% of terpenes were released from the LBL nanocapsules during the first 2 h, with a progressive continuous release over time until reaching up to 95.68% after 20 h. The activity against Listeria innocua biofilms was consistent with the release curves of CAR and THY. A successive exposure of biofilms to ML followed by LBL nanocapsules ensured a 99.99% inhibition of biofilms for up to 6 h. It is thus confirmed that a successive application of nanocapsules is a promising strategy to ensure a long-term protection of food contact surfaces.