Jack in the Box Inc., headquartered in San Diego, plans to lay off 66 corporate employees, effective Jan. 4. The positions being eliminated are in areas including IT, finance & accounting, supply chain, and in the human resources and legal departments, company spokesperson Brian Luscomb said.

The reason for the lay-offs is twofold. First, the company, which was once about 20 percent franchised, is now about 94 percent franchised. Second, up until March, Jack in the Box owned Qdoba Mexican Eats, and supported both brands with a shared-services approach. Some of those employees rolled off the Jack in the Box payroll with the sale, but others remained as the company still had contractual agreements to support Qdoba until it staffed up.

“We’ve been anticipating these position eliminations for quite some time,” said Luscomb. “It’s not new news to the investment community or to our employees. All of the employees who will be impacted have known about this for several weeks, some even longer.”

The severance package the terminated employees will receive will offer a baseline of six months’ wages, regardless of how long the person was employed. Employees could also receive additional severance, said Luscomb, depending on their length of service, up to a maximum of 26 weeks. Additionally, the package includes a component for medical coverage and outplacement assistance.

“We’ve been very transparent with employees about the need to restructure and reduce G&A. We’ve discussed with everyone here what we expect our future will look like as we roll off agreements that require us to support QDOBA,” said Luscomb.

Jack in the Box has made a number of headlines recently. Last month, news surfaced that the company's franchisees were demanding the current CEO, Leonard "Lenny" Comma, and the rest of the leadership team, be replaced following a vote of "no confidence.” A few weeks later, Jana Partners, a New York-based hedge fund, disclosed it had trimmed its holdings in Jack in the Box, down to 1,831,007 shares from 2,050,325 shares during the second quarter. The activist investor also signed a confidentiality and standstill agreement in which the hedge fund agreed to keep confidential certain business information regarding the chain restaurant. The agreement expires on Dec. 14 unless the two parties terminate it sooner.

Late last year, Jack in the Box sold fast-casual brand, Qdoba, to New York-based private equity fund, Apollo Global Management Group, for $305 million.

There are over 2,200 Jack in the Box restaurants nationwide, and about 100 in San Diego. Qdoba, also a San Diego-based company, will be recruiting locally to staff up.