Partially fluorinated graphites synthesized at room temperature are capable of reversibly accommodating various molecules in the interlayer space. The structures and properties of these intercalation compounds depend on the fluorine content in the matrix and the nature of the guest. In this work, we compare the thermal stability and optical characteristics of (C 2 F x ) n with x = 0.92 and 0.87, intercalated with acetonitrile and 2-butanone. Density functional theory calculations accompany experimental studies. It is shown that guest molecules prefer to be located over the sp 2 -carbon regions remaining in the partially fluorinated graphene layers. The 2-butanone molecule has stronger interactions with the layers due to its larger length, flexibility, and the presence of carbonyl oxygen. As a result, this guest leaves (C 2 F x ) n matrixes at higher temperatures than acetonitrile. Different guest−host interactions cause a change in the electron excitations and photoluminescence of the fluorinated graphite intercalation compounds. In particular, the spectra are red-shifted when the matrices contain 2-butanone. This property can be used to create optical chemisensors based on partially fluorinated graphene layers.