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The use of hemp mortar as a bio-based insulation composite is widely promoted in the construction sector in France due to its environmental and hygrothermal advantages and the availability and low price of hemp fibers. Nevertheless, the use of such materials claims the consideration of the microbiological contamination that could lead to its degradation. Molds are known for their ability to modify locally the composition of hemp mortar by decreasing the pH level. That’s why the main objectives of the present work are, first, to expose the hemp mortar favorable conditions for mold growth, secondly, to investigate the proliferation of the mold filaments inside the hemp mortar sample and, then, to analyze the crystallographic composition. Experimentally, hemp mortar samples were exposed to high level of relative humidity during one year until the mold growth. The SEM observation allowed to follow the internal growth and identify the depth of the mold growth. Finally, the composition of the contaminated hemp mortar was studied by X-ray diffraction. The obtained results reveal that molds growth occurs not only on the surface but also in the depth. Nevertheless, as the mold growth started only after one year of high humidity exposure, a good resistance of studied hemp mortar towards molds was noted. Furthermore, the mineralogical composition analysis of the contaminated samples shows that the hydrates responsible for durability remained. These results provide data to better predict the durability of hemp mortars.