Multilayer encapsulation of bioactive compounds represents a cutting-edge advancement in nanotechnology and delivery systems, with wide-ranging applications in both therapeutic and food industries. A single bioactive delivery system targets a specific biological entity, minimizing undesirable effects, but its capabilities are limited when addressing complex organs with multiple biochemical processes and bioreceptors. Nano-micro technological capsules have evolved towards multilayer designs to accommodate multiple bioactive compounds in a single platform for gradual release at predetermined digestive sites. Layer-by-layer (LbL) electrostatic adsorption is a popular multilayer encapsulation method that can load multiple bioactive compounds and release them in a controlled way at different times and locations to achieve a synergistic effect. Nano- and micro-scale LbL capsule formulations are increasingly using plant-based proteins due to their non-toxic, environmentally friendly nature and several advantages, including high biocompatibility, biodegradability, sustainability, affordability, controlled release capability, and ease of manufacturing and modification. This manuscript reviews current research and advancements in plant protein-based LbL capsules and their interactions with nutraceuticals or bioactive ingredients. Furthermore, it explores whether the development of multi-layered nano- and microcapsules aligns with trends in bioactives and discusses future research and development strategies.