Valladolid (Spain) is a medium-size city (~300,000 inhabitants) that established a greenhouse (GHG) emissions reduction target in 2011 of 20% from 2010–2020. However, tracking the evolution of GHG in medium-size cities is challenging due to the general lack of compulsory data collection at this scale and issues with boundaries when attempting alternative estimates. Here, we propose and apply a novel method to estimate the evolution of GHG emissions due to energy consumption for the period of 2010–2019 in Valladolid, combining top-down and bottom-up data following a physical energy flows approach. The energy consumption of the city is estimated by main sectors and types of energies. The results show that, throughout the past decade, both total energy consumption and its sector end-use share did not significantly change: final energy consumption remained at around 24 MWh (86.5 GJ) per capita and was still highly dependent on fossil fuels, especially natural gas and oil products (over 70% of total energy supply). The GHG reduction by 2019 was ~11% with relation to 2010 and, thus, had not reached the set objective; in per capita terms, the GHG reduction was lower (~6%) due to population loss during the period. The trend, however, has not been monotone and has instead followed a U-shape strongly correlated with the economic crisis and subsequent recovery, suggesting that transition policies have had, at most, a modest effect on the overall results. The analysis shows, first of all, the limitations of statistical sources at a local level, both for energy and mobility, which do not allow more accurate results in identifying the main energy consumers to be reached; and, secondly, the need for strong decarbonization measures which have to be set urgently at all the relevant institutional levels. Reaching GHG neutrality in the city by 2050 requires reducing the GHG emissions by ~13%/year, which is ~20 times faster than for the 2010–2019 average of 0.6%/year.