Wood and wood-based products are extensively used in the building sector due to their interesting combination of properties. Fire safety and fire spread, however, are of utmost concern for the protection of buildings. Therefore, in timber structures, wood must be treated with fire-retardant materials in order to improve its reaction to fire. This article highlights the flame retardancy of novel hybrid organic–inorganic halogen-free coatings applied on plywood substrates. For this purpose, either a huntite-rich mineral (H5) or its modified nano-Mg (OH)2 type form (H5-m), acting as an inorganic (nano) filler, was functionalized with reactive oligomers (ROs) and incorporated into a waterborne polymeric matrix. A water-soluble polymer (P (SSNa-co-GMAx)), combining its hydrophilic nature with functional epoxide groups, was used as the reactive oligomer in order to enhance the compatibility between the filler and the matrix. Among various coating compositions, the system composed of 13% polymeric matrix, 73% H5 and 14% ROs, which provided the best coating quality and flame retardancy, was selected for the coating of plywood on a larger scale in one or two layers. The results indicated that the novel plywood coating systems with the addition of ecological coating formulations (WF-13, WF-14 and WF-15), prepared at two layers, reached Euroclass B according to EN13501-1, which is the best possible for fire systems applied to wood.