A number of questions were raised regarding Councilor Dan Darnell's involvement as the nonprofit organization's executive director.
Darnell remanded himself from the discussion and vote, citing his conflict of interest.
Councilor Mary Fischer expressed her support for the organization's work in the community but asked if any rules were bent because of Darnell's position on the City Council.
City Manager Rob Mayes denied the allegations.
"I completely disagree with any allegations or questions regarding any preferential treatment," he said. "I haven't felt any pressure to provide any resources to (San Juan Safe Communities) that are not expressly called for in the terms of the contract."
The city opened proposals for a $40,000 contract for substance abuse and gang activity suppression services on Sept. 13.
Twenty-one companies were notified of the services request, according to a memo to the city's Central Purchasing division. Only one organization responded: San Juan Safe Communities Initiative.
Mayor Tommy Roberts removed himself from voting because of his involvement on the organization's board.