Stone-built cultural heritage faces threats from natural forces and anthropogenic pollutants, including local climate, acid rain, and outdoor conditions like temperature fluctuations and wind exposure, all of which impact their structural integrity and lead to their degradation. The development of a water-based, environmentally-friendly protective coatings that meet a combination of requirements posed by the diversity of the substrates, different environmental conditions, and structures with complex geometries remains a formidable challenge, given the numerous obstacles faced by current conservation strategies. Here we report the structural, electrical, and mechanical characterization, along with performance testing, of a nanostructured hydrophilic and self-healing hybrid coating based on hydroxyapatite (HAp) nanocrystals and polyelectrolyte multilayers (PEM), formed in-situ on Greek marble through a simple spray layer-by-layer surface functionalization technique. The polyelectrolyte-hydroxyapatite multilayer (PHM) structure resembled the design of naturally forming trabecular bone, attained at a short procedural time. It exhibited chemical affinity, aesthetical compatibility and resistance to weathering while offering reversibility. The proposed method is able to generate micron-sized coatings with controlled properties, such as adhesion and self-healing, leading to less weathered surfaces. Our results show that the PHM is a highly effective protective material that can be applied for stone protection and other similar applications.