Detection and identification of the microorganisms involved in biodeterioration of cultural heritage materials is vital. Since some artworks have an incalculable value, the use of nondestructive sampling methods is preferred. In this study, the possibility of using RNA-FISH technique for detecting microbial cells with low RNA content, isolated from biodegraded cultural heritage materials, was investigated. So, the possibility of the RNA-FISH protocol implementation as a noninvasive approach was studied. Wood and stone slabs artificially inoculated with yeast and bacteria cells were prepared and different sampling methods were applied to evaluate their performance regarding: i) the number of cells extracted and ii) the signals obtained by the RNA-FISH technique. It was possible to conclude that is possible to apply RNA-FISH for detecting cells with low RNA content and is possible to use noninvasive sampling in wood or stone materials.