The Cambridge City Council has cleared the way for another million square feet of development in booming Kendall Square, in exchange for a big dose of affordable housing, $6 million in transit funding, and low-cost space for startups.

The council voted Monday to rezone three blocks around the Kendall Square MBTA station to enable an additional 400,000 square feet of housing and 600,000 square feet of office and retail space. Most of the site is controlled by Boston Properties Inc., which already operates 2.7 million square feet of office space in the neighborhood and is also a major real estate owner in Boston, New York, Washington, and San Francisco.

The move will open up development in the region’s hottest business district, a place with office rents unseen this side of Manhattan and availability very scarce. In exchange, Cambridge officials say, it will bring much-needed housing, open space, and perhaps even a long-desired grocery store to Kendall.

“We think it’s a good plan,’’ said Tom Evans, executive director of the Cambridge Redevelopment Authority.

Boston Properties hasn’t detailed what it might build, or when it would start. Any specific projects would still need to be approved by the city’s Planning Board.

But city officials say that they expect most of the new development will be on under-built sites along Binney Street north of Broadway, and that biotech giant Biogen Inc. is a likely tenant for the commercial space. A Boston Properties spokeswoman did not return messages seeking comment Tuesday.

For the city, the rezoning was an opportunity to write some big priorities into law from the start.

The measure passed Monday requires that 25 percent of housing in the area — 140 units out of an estimated 560 — be affordable to low- or middle-income tenants, well above the 15 percent Cambridge requires in most new developments. It also mandates that 10 percent of commercial space be set aside for startups, with one-fourth of that at below-market rents. It lowers parking requirements and establishes incentives for grocery stores and pharmacies. And Boston Properties agreed to pay $6 million into a new transit fund to help improve public transportation in Kendall Square.

Those terms evolved through months of negotiations between Boston Properties and city staff. And while some at Monday’s meeting urged the City Council to push for more, council member Marc McGovern said Boston Properties had met the city’s demands.

“We pushed for 25 percent affordable housing. We got it,’’ he said. “We pushed for 25 percent subsidized innovation space. We got it. We pushed for below-market retail. We got it.’’

Now the City Council will turn its attention to another big site next door. Members are also mulling new zoning guidelines for the site of the Volpe transportation center, a 14-acre parcel immediately to the east.

The federal government is seeking a partner to redevelop that site, and a bevy of major Boston and national developers have signaled their interest. Council members will probably take up new zoning guidelines — which will also include higher affordable housing requirements and likely taller buildings than are now permitted — at the start of the year.

Tim Logan can be reached at tim.logan@globe.com. Follow him on Twitter at @bytimlogan.