Graham's resignation, which comes after only 14 months on the job, comes at a crucial time for the city-owned nonprofit agency, which has been trying to shift its attention from downtown redevelopment projects to infrastructure improvements in outlying neighborhoods.
Lori Young, the agency's administrative services manager, said she has already been working with Graham and other staff members on a transition plan.
"We are hopeful to have an interim team in place in the near future, and a permanent replacement within six months," she said.
Mayor-Elect Kevin Faulconer praised Graham as a "force for positive change" and said he looks forward to working with the agency "to continue the mission of creating vibrant, sustainable and thriving San Diego neighborhoods."
But Graham's departure could bolster the voices of the agency's critics, who have long complained that it is too tied to downtown developers.
Civic San Diego was created as a merger of the Centre City Development Corp. (CCDC) and Southeastern Economic Development Corp. (SEDC), which were in charge of allotting and distributing state funding for local redevelopment projects, ranging from affordable housing to Petco Park and the Convention Center.
When Graham -- previously director of real estate economics for the Guidant Group -- joined CCDC as vice president for redevelopment in 2007, it was on the verge of tumultuous changes.
In 2008, the agency was racked with scandal when it was discovered that then-president Nancy Graham (unrelated to Jeff) had not reported $3.5 million of income on her financial statements, prompting her resignation. The post remained vacant until Graham was appointed to it four years later.
In the meantime, Gov. Jerry Brown announced he was putting an end to the state redevelopment program that had provided the agency with its funding, putting an end to CCDC, SEDC and similar agencies throughout the state once they were finished funding projects in their pipeline.
When Graham was named to head the agency in October 2012, however, he was encouraged by then-Mayor Jerry Sanders and other civic leaders to take the agency in another direction: seeking new ways of funding developments beyond downtown.
Over the past year, Graham has suggested using state and federal redevelopment grants, regional transportation funds and investments from financial institutions to spur development in neighborhoods such as City Heights, Logan Heights, Encanto and San Ysidro.
The Downtown San Diego Partnership last October gave him an award for his "well-deserved reputation for coming up with bold and thoughtful financing strategies to help make big projects happen."
Critics say that Graham's ideas for Civic San Diego might duplicate or conflict with the planning and permitting work already done by the city's newly reinvigorated Planning Department and Development Services Department and might also lack the accountability of those public agencies.
When Graham aired his proposal before the City Council last year, Councilmember David Alvarez stressed that he wanted to make sure the agency would be "accountable to each and every neighborhood in the city."
On the other hand, a white paper from the Urban Land Institute said Civic San Diego, with its focus on securing public and private funds for development projects, could complement the planning work being conducted by City Hall, as long as the agencies all work collaboratively.