CONCORD — Lennar Urban will get the first shot at transforming the Concord Naval Weapons Station into a thriving community with housing, parks, retail and office space.

During a special meeting Wednesday, the City Council voted unanimously to select Lennar as master developer of the first phase of the multimillion-dollar project, which includes approximately 500 acres of the former military base.

The decision ends a tumultuous period in Concord, during which allegations of influence peddling and backroom deal-making rocked City Hall and undermined public confidence in the integrity of the developer selection process.

“I think this is a great deal, I think it is beneficial to all concerned, I think it’s a fair deal,” Councilman Edi Birsan said.

Council members Tim Grayson and Ron Leone did not attend the meeting, because they have recused themselves from voting on the master developer.

The next step is negotiating the formal contract, known as a disposition and development agreement, which could take six to nine months. Lennar has agreed to initiate and pay for the land use plan and environmental studies while the two parties hammer out the contract.

“We are very grateful for this opportunity,” Lennar regional vice president Kofi Bonner said in a written statement. “There is a lot of work ahead of us, but I can assure you that we are committed to working with city staff, the U.S. Navy and the people of Concord to remake the naval weapons station into a vibrant new area that will make this city proud.”

The city reopened negotiations with Lennar in March after Catellus Development Corp. withdrew from consideration.

In its revised financial proposal, Lennar agreed to spend nearly $16 million to widen Willow Pass Road to four lanes and rebuild Willow Pass bridge as a four-lane span, and spend $40 million for affordable housing, which — combined with other funding sources — would ensure that 810 units are built, the company has said.

But Lennar also reduced by $10 million the guaranteed payout Concord would receive to $20 million over 10 years. Once Lennar earns a 20 percent return on its investment, it will share the profits, which could amount to an additional $23 million for the city.

Mayor Laura Hoffmeister said Lennar’s guaranteed cash is better than tying the city’s share solely to the project’s financial performance.

“I’m looking for something that’s more conservative and I’m willing to make sure that we get something that’s for the benefit of the community that we can count on,” she said.

Lennar’s proposal also allocates $39 million for a K-8 school; $26 million for 80 acres of parks, greenways and open space; $20 million for two community centers; and $3 million for a shuttle connecting the development to Todos Santos Plaza.

The Concord Reuse Project Area Plan calls for building up to 12,272 housing units and 6.1 million square feet of commercial space on about 2,300 acres of the former military base. The Navy is scheduled to begin transferring land to the city in the spring of 2017.

Concord delayed the decision for months to look into Catellus’ allegations that Lennar had engaged in improper lobbying. An independent investigator concluded that Lennar had engaged in lobbying by soliciting donations to former Mayor Tim Grayson’s Assembly campaign.

“Given a project of this magnitude and complexity, it’s to be expected that mistakes would be made and they were,” Councilman Dan Helix said. “The train went off the tracks.”

But he praised city staffers for working diligently with Lennar to improve its offer, particularly with respect to providing funds for affordable housing and bonds ensuring that the infrastructure is built.

Rather than transfer the entire 500 acres of the first phase to Lennar at one time, the city will turn over individual parcels when Lennar is ready to begin development, and the company demonstrates that it has the funds to do the work, posts bonds and secures insurance.

Lennar also agreed to share annual project revenues, profits, costs and net cash flow information with the city.

Although the company won over Helix, a few skeptical residents urged the council to reject Lennar and begin a new search for a master developer.

“I still don’t feel comfortable with Lennar,” said Ralph Oliver, a 24-year Concord resident who lives in the Sun Terrace neighborhood. “The more I learn about Lennar, the more I feel that they will act unethically whenever it suits them.”

Lisa P. White covers Concord and Pleasant Hill. Contact her at 925-943-8011. Follow her at Twitter.com/lisa_p_white.