Municipalities play a vital role in the energy transition through investments that support the development of a low-emission economy. The intensity of such activities varies spatially and is shaped, among other factors, by proximity to large urban centers. The main objective of this study is to assess the relationships between the functional linkages of rural and urban–rural municipalities with larger urban centers and the level of investments in a low-carbon economy co-financed by European Union funds in the periods 2007–2013 and 2014–2020. The analysis applies a classification of municipalities based on their inclusion in Functional Urban Areas (FUA) and the Delimitation of Rural Areas (DOW). The hypothesis assumes that municipalities located within FUAs exhibit higher investment levels than those outside. The results confirm higher activity, especially in low-density municipalities near metropolitan areas. The hypothesis is partially supported: proximity to urban centers is associated with higher investment levels in spatial terms but does not always translate into higher per capita expenditure.