This study concerns the investigation of pigments and efflorescence phenomena on the wall paintings of Kastoria, a rural, non-metropolitan Byzantine town. A large number of representative samples were collected from the murals of three churches, dated to post-Byzantine era (14th-17th c. AD). The identified pigments for the red colour were hematite (Fe2O3), cinnabar (HgS) and minium (Pb3O4), while brown and yellow colours were attributed to mixtures of ochres (Fe-oxides and hydroxides) and lime. The utilization of admixtures of iron, lead and mercury compounds was also attested in order to render specific tones on the painted surfaces. Black and dark blue hues were prepared using black carbon and Mn in some cases. Grey colours were assigned to a mixture of black carbon and lime. Green colour is rather attributed to admixtures of Fe-rich minerals and lime and not to the commonly used green earths. Baryte (BaSO4) was also evidenced as a filler or extender. Phosphorous was detected and connected to proteinaceous material and Mo and Sb were traced which are probably affiliated to Fe-oxides. Regarding efflorescing salts, the determined compounds are: calcite, dolomite, gypsum, halite, nitratine, natron and mirabilite, all of which are related to temperature and humidity changes and moisture fluctuations inside the wall paintings.