In smaller components of industrial or energy automation systems, such as device controllers of Protection and Control (PAC) systems in smart grids, controller functionality is tightly coupled with the physical device or sensor capabilities. At this level, software is small and therefore easy to maintain and test. However, when multiple controllers are interconnected and higher-level functionality is added, software applications grow exponentially, and ensuring maintainability becomes proportionally challenging. In this paper, we extend the IEC 61499 reference architecture used to develop industrial automation software with the principles of Abstraction Layered Architecture (ALA) that has shown up to 400% improvements in industrial software maintainability. We show that even a light application of abstraction layering on the top, application-level of IEC 61499 applications makes them significantly more readable and slightly more maintainable. More concrete gains in maintainability are expected when abstraction layering is integrated into lower layers.