In recent years, there has been a growing interest in exploring environmentally friendly and healthy alternatives to conventional solvent cleaning and biocides in the conservation of stone artworks. Here, we focus on the potential of laser-based photonic methods for treating biodeteriorated earthenware artefacts. The investigation was conducted on Roman dolia (jars) of the International Museum of Ceramics, Faenza, Italy. Three removal methods were tested and compared: (i) brushing using a soft-bristled electric brush and water, referred to as brush cleaning; (ii) a combination of brushing and laser ablation; and (iii) biocide and brushing. Four laser systems with different wavelengths and optimized pulse durations in nanosecond or microsecond regimes were used in the tests. Systematic irradiation tests were conducted to determine the damage thresholds and define safe laser irradiation levels. The characterizations of the surfaces under treatment were carried out pre- and post-laser irradiation using optical microscopy, 3D photogrammetry, and Pulse-Amplitude-Modulated Chlorophyll-Fluorometry. Furthermore, spectroscopic methods based on FTIR, Raman, and LIBS techniques were used to assess the effectiveness of the removal process and the composition of uncovered surfaces. Results have indicated that gentle brushing and water is the most effective approach for safely removing around 60% of the bio-colonization weakly anchored to the substrate over the area under treatment. This comprised viable species, whereas the remaining 40% of the area included endolithic species, mostly thalli of Verrucaria nigrescens and rock-dwelling fungi. The eradication of the latter was the real conservation concern requiring attention. Following the experimentation, the optimal method for safely uncovering the earthenware surface was a combination of water-assisted brushing and 1064 nm laser irradiation as a finishing treatment.