The research focuses on analyzing the production techniques and materials of a Roman paint-plastered ceiling from a Late Antique Roman villa near Negrar (Verona, Italy), recently uncovered. Stylistic features of the decoration, found in reworked collapse debris during the villa’s excavation, date the ceiling to the original construction phase in the 4th century CE. The paper presents the protocol we adopted for recovering and analyzing the painted decoration of the villa, which was in-laboratory recomposed in its original layout after a meticulous and systematic retrieval of fragmented materials. Microsamples of mortar and pigment were then taken to fully reconstruct the execution technique and raw materials used in the paint-plastered ceiling, detailing the application of the tectorium and pigment preparation. Mortar samples were analyzed to define preparatory layer properties, using various analytical techniques including Transmitted-Light Polarized Optical Microscopy (TL-OM) and Scanning Electron Microscopy with Energy Dispersive X-Ray Analysis (SEM-EDS). Optical reflected-light microscopy detected guide incisions on the preparatory mortar, while Reflected-Light Optical Microscopy (RL-OM) revealed the microstratigraphy of pictorial micro-layers. Micro-samplings of painted decorations were conducted to define pigment palettes, determining their mineralogical composition through X-Ray Powder Diffraction (XRPD) analysis coupled with micro-Raman analyses for the determination of carbon-based compounds. The research aims to establish a comprehensive protocol for future endeavors, integrating archaeological reassembly with precise micro-analyses of pigments and mortars, deciphering the intricate layout of ancient, fragmented decorations. This study is the first of its kind in Northern Italy, overcoming challenges posed by fragmented and reworked artifacts in previous research, enabling detailed analytical studies like those conducted here. Moreover, this study of the paint-plastered ceiling of the Late Roman villa of Negrar aims to provide a new impulse for the knowledge of Late Antique painting techniques and materials, which were only marginally considered within Roman painting tradition so far.