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The global COVID-19 outbreak has demanded drastic actions and policies from the governments and local authorities to stem the spread of the virus. Most of the measures involve behavioural changes from citizens to reduce their social contact to a minimum. Thus, these actions influence individual activity patterns and transport systems in different ways. This paper studies the short-term impacts on the transport system caused by the different policies adopted by the Colombian government and local authorities to contain the COVID-19 spread. Using official and secondary data concerning the seven most populated cities in Colombia, we analyse the impacts on three components of the transport system: air transport, freight transport, and urban transport. Results show that national policies and local decisions have decreased the demand for motorised trips across the cities, diminishing congestion levels, reducing transit ridership, and creating a reduction in transport externalities. The country banned air transport for passengers and only allowed air cargo for medical and necessary supplies, which will have negative consequences for the economics of the airline industry. During the first three months of the COVID-19, freight was the most resilient transport component. However, freight trips diminished around 38%, affecting mainly the supply chain of nonessential products. During the pandemic, governments need to provide subsidies to maintain the system supply to avoid crowdedness and promote active transport by allocating less-used street space to cyclists and pedestrians. In the short term, transportation service providers will face a financial crisis, deepened by the pandemic, which will require government assistance for their recovery. [ABSTRACT FROM AUTHOR]