The Arlington County Board agreed Tuesday to allow Boeing to build a six-story regional and international headquarters, instead of a mixed-use development, on county-owned land near the Pentagon and Reagan National Airport.

The aerospace firm, a major regional employer, will build the 453,000-square-foot secure facility, with two floors of underground parking, just north of Crystal City near the Roaches Run wildlife refuge, on Old Jefferson Davis Highway and South Sixth Street. Construction is expected to begin next month and will merge two offices at one location. A 45-room motel and five warehouses on the site are currently vacant.

The county previously agreed to exchange its 4.7-acre site for 7.09 acres at the north end of Long Bridge Park, where it plans to build an aquatics, health and fitness facility.

Boeing will pay $1.5 million for affordable housing and $150,000 for transportation mitigation; install a Capital Bikeshare station; improve its landscaping plans and allow public access to its lawn; and reach a gold-certified building standard for energy efficiency.

Allowing a single user in a glass-encased building violates the county’s preferences for mixed residential, retail and office use. Residents and advisory commissioners objected to that as well as to other aspects of the development, including the impact on traffic and the corporate sign atop the building, but the County Board determined that the importance of keeping Boeing in the area outweighed those issues.

“There’s an old saying that nothing worth doing is easy. . . . This proposal was not without controversy,” County Manager Barbara Donnellan said at the three-hour discussion of the proposal. “The retention of 500 jobs is huge. . . . The economic benefits to this are, to me, tremendous. A GSA tenant would pay no taxes. . . . [Boeing] will be part of our community and paying taxes.”

The Arlington County Board also approved up to $13.26 million in loans from the Affordable Housing Investment Fund to help AHC Inc., a nonprofit affordable-housing developer, buy and renovate the 198-apartment Magnolia Commons complex on Columbia Pike. The apartments were built in 1947 and are considered one of the county’s historic sites.

AHC has a contract with CMG LLC to buy the property for $35 million. The County Board also authorized up to $32 million in revenue bonds by its industrial development authority, secured by the net revenues of the Magnolia Commons project and thus not a county obligation.

The tenants at Magnolia Commons, most of whom will be eligible to stay in the housing after it is renovated, will be eligible to share a $594,000 fund for relocation expenses.

In another matter, residents can expect more bikes and bike stations in Arlington now that the County Board authorized spending $1.2 million in federal funds to expand the Capital Bikeshare system by 30 stations and 192 bikes.

When the stations are completed next summer, there will be 70 in Arlington County.