Buildings have become a key source of greenhouse gas (GHG) emissions due to the consumption of primary energy, especially when used to achieve thermal comfort conditions. In addition, buildings play a key role for adapting societies to climate change by achieving more energy efficiency. Therefore, buildings have become a key sector to tackle climate change at the local level. However, public decision-makers do not have tools with enough spatial resolution to prioritise and focus the available resources and efforts in an efficient manner. The objective of the research is to develop an innovative methodology based on a geographic information system (GIS) for mapping primary energy consumption and GHG emissions in buildings in cities according to energy efficiency certificates. The developed methodology has been tested in a representative medium-sized city in Spain, obtaining an accurate analysis that shows 32,000 t of CO2 emissions due to primary energy consumption of 140 GWh in residential buildings with high spatial resolution at single building level. The obtained results demonstrate that the majority of residential buildings have low levels of energy efficiency and emit an average of 45 kg CO2/m2. Compared to the national average in Spain, this obtained value is on the average, while it is slightly better at the regional level. Furthermore, the results obtained demonstrate that the developed methodology is able to directly identify city districts with highest potential for improving energy efficiency and reducing GHG emissions. Additionally, a data model adapted to the INSPIRE regulation has been developed in order to ensure interoperability and European-wide application. All these results have allowed the local authorities to better define local strategies towards a low-carbon economy and energy transition. In conclusion, public decision-makers will be supported with an innovative and user-friendly GIS-based methodology to better define local strategies towards a low-carbon economy and energy transition in a more efficient and transparent way based on metrics of high spatial resolution and accuracy.