The 62-year-old president addressed a crowd of 2,000 at his inauguration, using the opportunity to send a message to the the Revolutionary Armed Forces of Colombia and the left-wing members that have continued their attacks.
"Gentlemen of the FARC: you have been warned."
Santos' re-election campaign focused on his determination to end Colombia's decades of conflict and negotiate a peace with the FARC.
At his inauguration, Santos reiterated his dual approach to FARC, telling those gathered, "We will continue fighting because the fastest way to reach the end of this conflict is not to cede even a centimeter of our territory while we continue negotiations abroad."
Negotiations are expected to resume August 17 in Havana.
The conflict between the government and the FARC began in the 1960s and is considered Latin America's longest running conflict. An estimated 220,000 people have been killed and three million internally displaced by the fighting.