Heritage sites are affected by many factors that cause degradation and decay over time, such as soil deformation, changes in weather conditions, or excess moisture, which can cause damages to historical sites. For this reason, restoration works are planned and carried out to preserve the object's existing condition, renovate and repair the damaged parts, or restore the original condition of the object. The Rescue Project was undertaken in the Blessed Ladislas’ chapel in St. Anna's Church in Warsaw, Poland. The main goal of the planned work was to restore the original rococo character of the dome paintings. The aim of this article was to present the integration of the multi-temporal conservation work and non-invasive measurements for changes analysis during conservation works. For this purpose, point clouds acquired with a Z+F 5006h ground-based scanner and images captured via Structure-from-Motion and MultiView Stereo method implemented in Agisoft Metashape software were used. The proposed conservation analysis method was a multi-stage process that involved: (1) automatic data integration using a feature-based approach based on 2D detectors and point clouds converted to spherical images, (2) generalisation and harmonisation of source data, and (3) analysis of deviations between point clouds. Having registered point clouds with each other, it was possible to analyse changes that occurred during conservation work. Calculated distances between both point clouds show the localisation of cracks and damages and enable measure of the size and depth of crevices on the dome wall.