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I have a project in QGIS comprised of shapefiles and raster maps. The origin CRSs are mostly on ETRS89 / Portugal TM06. I am trying to convert the project to WGS84 to have lat/lon instead of metric values on the map coordinate labels.

However, I cannot do it. I have enabled on-the-fly transformation after choosing WGS84 EPSG:4326 but still cannot get lat/lon coordinates in the coordinates window in the bottom of QGIS screen or on map coordinates in Print composer. All my layers are on WGS84 (EPSG:4326).

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Don't set the layer CRS to WGS84 if they are in ETRS89! You are giving QGIS the misleading information that these layers contain data in WGS84 and therefore QGIS won't reproject the geometries anymore because it thinks they already are in degrees.

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