Sepiolite is a fibrous clay mineral and consists of 2:1 silicate blocks connected at the corners and separated by tunnels (channels on external surfaces) that extend in the direction of fiber length. The tunnels, 3.7 Å × 10.6 Å in cross-section, are responsible for the incorporation of organic and inorganic compounds. The present study aimed to examine the capacity of twelve different organic molecules, such as pyridine, indigo, methylene blue, and quaternary amines, to gain access to the tunnels of sepiolite using quantum chemistry techniques. The interaction energy computations performed at the B97-D/TZVP level showed that all of the considered organic molecules tend to access the tunnels of sepiolite if external water molecules are absent. This finding is in agreement with experimental studies that included pyridine, indigo, 2,2-bipyridyl, and methylene blue. Interestingly, 2,6-dimethyl pyridine preferred to remain in a tunnel rather than an external channel of the sepiolite.