Sant Quirze de Pedret is a Romanesque church located in Cercs (Catalonia, Spain) at the foothills of the Pyrenees. Its walls harbored one of the most important examples of mural paintings in Catalan Romanesque Art. However, in two different campaigns (in 1921 and 1937) the paintings were removed using the strappo technique and transferred to museums for safekeeping. This detachment protected the paintings from being sold in the art market, but at the price of breaking the integrity of the monument. Nowadays, the paintings are exhibited in the Museu Nacional d'Art de Catalunya - MNAC (Barcelona, Catalonia) and the Museu Diocesà i Comarcal de Solsona - MDCS (Solsona, Catalonia). Some fragments of the paintings are still on the walls of the church. In this work, we present the methodology to digitally reconstruct the church building at its different phases and group the dispersed paintings in a single virtual church, commissioned by the MDCS. We have combined 3D reconstruction (LIDAR and photogrammetric using portable artificial illumination) and modeling techniques (including texture transfer between different shapes) to recover the integrity of the monument in a single 3D virtual model. Furthermore, we have reconstructed the church building at different significant historical moments and placed actual paintings on its virtual walls, based on archaeological knowledge. This set of 3D models allows experts and visitors to better understand the monument as a whole, the relations between the different paintings, and its evolution over time.