The Philippines entered its most prolonged lockdown in 2020 when the coronavirus disease (COVID-19) became a pandemic. Additionally, there has been a shift from physical to online classes at all education levels. Against this backdrop, the restrictions imposed on the education sector could have environmental impacts, including on the carbon emission structure. Here, we compare the carbon footprint before and during the pandemic, determine how the pandemic changed the activities that directly affected carbon emissions, and present reduction methods to minimise emissions in the new normal. We calculated emissions before and during the pandemic to achieve these goals, using the data obtained from University of the Philippines (UP) Cebu. The total CO2 emissions of UP Cebu in 2019 were estimated to be 1420.7 tCO2e, which did not significantly differ from the 2018 emissions. In 2020, the total CO2 emissions were estimated to be 555.8 tCO2e, equivalent to a 60.9% decrease from the 2019 emissions. The per capita emissions in UP Cebu for 2019 and 2020 were estimated to be 0.9 tCO2e and 0.3 tCO2e, respectively – both below the national average. The pandemic caused a significant decrease in emissions per activity, except for emissions from fuel, which increased 305.8%. In the post-COVID-19 world, especially when in-person classes return, UP Cebu must consider concrete strategies to curb its emissions. Specific decarbonization methods for each activity were simulated and discussed. The results and reduction strategies presented are relevant to UP Cebu and other higher education institutions in the Philippines and Asia with the same characteristics.