Affordability requirements for 85 units in Boston’s Mercantile Wharf apartments are scheduled to expire in 2018 as a 40-year state-subsidized mortgage is retired. Housing officials are using a variety of incentives to preserve more than 3,000 affordable units in similar properties across Massachusetts.

The financing package that enabled a nonprofit to preserve 52 units of affordable housing in Boston’s Fenway neighborhood was characteristically complex, tapping multiple sources to fill the gap between acquisition costs and future rental income.

In the wake of Fenway Community Development Corp.’s $15.2 million acquisition of the Burbank Gardens complex, all of the units will remain income-restricted, including 39 apartments reserved for households earning no more than 60 percent of the area median income. In a rapidly gentrifying neighborhood, Burbank Gardens residents otherwise would have faced conversion of their units to market-rate rents within three years.

It’s a scenario playing out at 32 privately owned housing complexes across the state that participated in the state’s Section 13A mortgage program. Deeply affordable rents – available to households making 30 percent to 50 percent of area household median income – are being lifted as the 40-year mortgages expire. From now until 2020, nearly 3,100 units are at risk of conversion to market rate rents.

“We don’t want to lose these really important affordable housing properties,” said Sheila Dillon, Boston’s director of neighborhood development. “A lot of them are in downtown locations and are very hard to replace.”

Affordability requirements will expire at a half-dozen properties in Boston containing nearly 300 units in the next three years. Included are 85 units in the Mercantile Wharf apartments in Boston’s North End and 160 units in the Babcock Tower in Allston. Unlike properties with expiring federal mortgage subsidies, residents of 13A properties are not eligible for federal vouchers that could be used at other properties.

City housing officials have contacted all of the remaining properties and are in negotiations with some of them on agreements to preserve all or some of the affordable units, Dillon said.

“It’ll cost us, and that money is going to take away from new (affordable housing) production,” she said.

DND chipped in $5 million toward the financing package at Burbank Gardens, and Dillon said the department expects to contribute similar amounts in coming years to other at-risk properties. MassHousing’s board voted in 2016 to commit $50 million to preservation of 13A units.

As an alternative to CDC acquisitions, housing officials have worked with some developers to implement rent control for current tenants while allowing units to convert to market rents as units turn over. That was the arrangement used at the 31-unit Paul Revere Court apartments in Boston’s North End.

Allston-Brighton Community Development Corp. is seeking to save 160 income-restricted units in the 213-unit Babcock Tower across from Boston University’s West campus. The property is owned by Natick-based Franchi Management and the mortgage expires in 2019.

“There’s a lot of elderly and disabled people in those buildings, and we’re very worried about how that’s going to go and where they’re going to move,” said Carol Ridge Martinez, executive director of the Allston-Brighton CDC. “At this point, it’s looking like the tenants will have to eventually be relocated.”

Long-Term Plans For Preservation

Protecting the existing inventory has been a collective effort in recent years by state housing agencies, nonprofits and local communities. Since 13A mortgages began expiring in 2012, the state has preserved nearly 4,000 affordable units in 36 developments.

Anticipating the wave of affordability expirations, state legislators in 2009 enacted Chapter 40T, which caps rent increases following 13A mortgage expirations. It requires owners to notify state and local officials if they’re selling the property. And it gives the state Office of Housing and Economic Development the first shot at acquiring the property, or designating another buyer such as a private developer or nonprofit.

Boston-based Community Economic Development Assistance Corp. (CEDAC) also plays a key role by providing short-term acquisition financing and technical assistance to community development corporations looking to acquire 13A properties.

At Burbank Gardens, CEDAC granted an 18-month, $8.3 million acquisition loan, which Fenway CDC expects to convert to permanent financing next year. The agency typically lends between $20 million and $25 million a year for such projects as underwriter of state housing bond programs, Executive Director Roger Herzog said.

“13A is the first program where there were no federal vouchers being offered, so tenants were very vulnerable,” Herzog said.

At Burbank Gardens, 39 units will be retained for households earning a maximum 60 percent of the area median income. Nine will be set aside for households earning 80 percent of AMI, and four will be preserved at 90 percent of AMI.

The financing package includes the city’s $5 million contribution, $5 million in acquisition debt from MassHousing, a $3.8 million construction and permanent tax-exempt bond financing and a $5.4 million bridge loan.