The archaeological site of Eynan, located by the spring of Ain Mallaha and on the shores of Lake Hula in the Upper Jordan Valley, Israel, existed for several millennia at the end of the Pleistocene. During the Natufian culture of the Levantine Epipalaeolithic, the site was one of the largest known occupations in the Levant for some millennia (ca. 14,300 -11,900 cal BP). Remains of Natufian architecture were found, together with evidence of early experimenting with pyrotechnology for the creation of lime plaster. Several features were identified during the excavations as assumed lime plaster installations. Samples investigated by micromorphology methods under the polarizing microscope revealed that while all were composed of calcium carbonate, and some indeed represent anthropogenic burnt lime products, others reflected the results of post-depositional or contemporaneous natural processes rather than technological products. The study of the samples at a molecular level through Raman spectroscopy enables a new methodology for the quick distinction between the features observed by micromorphology.