Terrestrial laser scanning (TLS) is a three-dimensional survey technique proven successful for in-field stratigraphic and site-wide documentation or damage assessment of archaeological heritage. This study explores the potential utility of TLS and the Multiscale Model to Model Cloud Comparison (M3C2) surface change detection method for monitoring and preserving ancient earthen architecture, and for creating comprehensive site monitoring programs in compliance with UNESCO periodic reporting guidelines. The proposed methodology was tested using 3-D TLS datasets spanning a period of six years to assess the decay of mud brick structures at Çatalhöyük, Turkey in order to understand material loss in walls and buildings, identify potential underlying causes, and create a plan for physical interventions. This paper explains how a multi-temporal laser scanning workflow using the M3C2 method can be leveraged successfully to quantify—with millimeter-level accuracy—the decay of large earthen sites and inform future conservation interventions. This approach allows for the identification of the wall features with the most immediate risk of deterioration based on the detection of patterns of change and calculation of its significance as a preventative measure. Results presented in this paper suggest that the proposed method can be used effectively to enhance site monitoring and perform preventative on-site interventions at large earthen sites earthen sites in the Middle East, Africa, Europe, and the Americas.