Recent studies of churches of medieval origin in Estonia have shown that these edifices have long histories of polychrome decoration both before and after the Reformation. In this article, some aspects of these colour schemes are discussed. Firstly, the question of the decoration and redecoration of interiors during the Middle Ages is addressed, secondly the authorship and technique of vernacular looking murals is discussed, and thirdly the geographical spread of these decorations is analysed. In addition, post-medieval murals are also examined. This article is based on fieldwork in Estonian medieval churches conducted over a period of fifteen years by the staff and students of the Department of Conservation and Cultural Heritage at the Estonian Academy of Arts. Here mainly the results of work in the churches at Koeru, Keila and Jarva-Jaani is presented. Some other churches are also discussed for comparison. So far, medieval painted decoration has been found in around 25 church interiors on the territory of present-day Estonia, i.e. in roughly a quarter of the medieval churches. Although the number is not large, the finds allow us to draw some conclusions regarding the spread of and networks behind these paintings. We can claim that as elsewhere in medieval (northern) Europe, medieval church interiors included at least some kind of painted decoration. It seems likely that the first (and possibly in many cases the only) colour scheme was provided by the builders. Especially in rural parishes, where no specialised guilds existed, it might have been difficult to employ professional painters, although not impossible. Almost certainly the decoration was applied at the time of plastering, when the mortar had not yet set and the scaffolding was still available. Historical records, surviving artworks and investigated interiors demonstrate that after the Reformation the Lutherans were less radical in transforming churches than were other Protestants: several Catholic altar retables and statues were preserved, side altars were not removed, etc. The churches were usually decorated with new, more modern murals and only whitewashed in many cases several centuries later. Gradually, church interiors became more monochrome, although not necessarily white, something that has been associated with the spread of Pietistic ideas in the Lutheran church. However, the late 19th century brought a revival of colour to at least some churches. These colourful, mainly Gothic revival interiors survived for only a short time and disappeared again when they were painted over everywhere. For example, in St Lawrence's in Kuusalu, wall paintings dating from the period of the Gothic revival renovation of the medieval church (1899) were found and uncovered in 2021.