<p>In 1985, the World Heritage Committee inscribed the site “Painted Churches in the Troodos Region” of the Republic of Cyprus on the UNESCO World Heritage List. The latter included nine Byzantine and Post Byzantine Churches to which a tenth church was added in 2001. In the framework of the IH-AT project, all the churches and the premises in their proximities were analysed using a wide array of non-destructive digital methodologies coupled with more traditional art-historical studies. Image- and Range-based techniques were used to document all the morphological features of the buildings with the final goal of understanding their humble architecture. Additionally, a Ground Penetrating Radar (GPR) was performed to investigate the presence of buried structures that, according to historical sources, were once surrounding the religious sites.</p><p>For the exploitation and visualization of the extensive database by the scientific community and the public at large, a web portal comprised of reliable and efficient technology-ready tools have been developed.</p><p>The proposed methodology was implemented to provide new insights on the churches’ architectural features; confirm the presence or absence of buried remains of archaeological interest; and help heritage professionals, with lack or minimal programming skills, to customize online visualizations of 3D interactive models.</p>