No one would argue that New York and Atlanta are very different markets. With low vacancy rates and high rent, New York has one of the strongest commercial-real-estate markets in the country. Atlanta, with high vacancies and lackluster rent growth, is one of the weakest among major cities.

Yet Jamestown Properties is testing its luck down South by applying a formula that it has successfully honed in New York, Boston, San Francisco and elsewhere: converting massive industrial buildings into fashionable properties filled with...