The summit will take place under tight security amid threats from a rebel group that has ramped up shooting and bomb attacks in towns around Cali in recent months, setting authorities on edge.
Cali Mayor Alejandro Eder said a car loaded with explosives was found and deactivated outside a church, with a health center and police station nearby.
"Thanks to the timely reaction of the police this morning we were able to prevent an apparent terrorist act in the El Vallado neighborhood, in the city of Cali," Eder said in a press statement.
"This is the fourth attempt at a terrorist act so far this year," he added.
Police commander Colonel German Cornejo said locals had alerted officers about a "suspicious" vehicle that had been "parked and running for several hours."
Some 12,000 delegates and exhibitors, as well as heads of state, are expected to take part in the summit from October 21 to November 1, in one of the world's most biodiverse countries.
Cali is the capital of the southwestern Valle del Cauca department, the main coca-growing region in Colombia, the world's largest cocaine producer.
The department is the stronghold of the Central General Staff (EMC) guerrilla group made up of fighters who broke away from the FARC movement when it signed a peace deal in 2016.
In July, the EMC warned the 16th meeting of the Conference of the Parties (COP16) of the Convention on Biological Diversity "will fail."
But, in August, the group decreed "the suspension of offensive military operations against public forces" in Cali.
Being granted COP16 host status was a major coup for Gustavo Petro, Colombia's first-ever leftist president, who campaigned on an ambitious conservation and climate change program.
Petro has seen his quest to achieve "total peace" in a nation struggling to emerge from decades of armed conflict bogged down in complicated negotiations with a variety of armed groups.
The EMC recently split into supporters of Petro's peace efforts and opponents led by a man known as Ivan Mordisco, who commands an estimated 2,000 fighters.
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