It is widely recognized that the design and application of suitable and robust science, technology and innovation (STI) policies and appropriate STI institutions promote development, economic growth and competitiveness in the long run. This paper analyses the dynamics of STI in Colombia over the 1995–2019 period to determine its relationship with its most important determinants and its collateral relationship with economic growth as an input affecting different issues; this work takes into account the creation of the new ministry of science, technology and innovation (MSTI) and uses different time series techniques. According to the analysis, a positive relationship exists between investments in research and development, STI activities, and the independence and transparency of STI management by the new MSTI, which could generate higher productivity, technological change, economic growth and development. The results of the models also demonstrate the long-run relationship and short-run dynamics related to STI investment and research results and the importance of transparency and independence. It is important to establish adequate STI governance and allow new ministries to play an important role to achieve a society based on knowledge that produces relevant research, technology and innovation based on the needs and resources of the country.