This paper presents the development of IgrejAR, an augmented reality platform designed to allow museum visitors to the National Azulejo Museum to experience the memory of the lost 16th-century church of Madre de Deus in Lisbon, Portugal. Through the integration of historical research, laser scanning, photogrammetry, and digital modelling, we have virtually reconstructed the original church believed to have been once housed within the space of the present D. Manuel Room. Building on five years of previous virtual reconstruction research, this paper examines the latest methodologies, challenges, and outcomes involved in reconstructing the church, with particular focus on the final integration of this knowledge into an AR environment. The research aims to provide a firsthand experience of the past by synthesizing diverse historical evidence—including chronicles, paintings, contracts, and archaeological findings. It presents the first complete visualization of the church’s interior, with all its known remaining artifacts reassembled and repositioned in their original location, despite their current dispersion in other collections. By leveraging markerless AR technology and the point cloud data used to create the digital model, the IgrejAR application offers minimal disruption to the current museum experience, allowing visitors to awaken the past on top of the present.