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Clover Fast Food Inc. paid over $79,000 in back wages and damages to 65 employees after the Department of Labor determined the company violated the Fair Labor Standards Act.

In a blog post, Clover owner Ayr Muir wrote Clover decided to settle with the department because it could not afford to bring the case to court. The department’s investigation into the restaurant chain stretched for more than four years, according to Muir.

Clover operates 12 locations in the greater Boston area, including restaurants in the Science Center, Harvard Square, and Central Square. The chain used to run a fleet of food trucks, but closed them down in summer 2017.

Muir wrote in his blog post that he found the investigation “disturbing.”

“We thought we were doing everything on the up and up,” he wrote. “From day 1 at Clover I’ve wanted us to adhere to all laws and regulations.”

The department calculated that Clover missed more than $39,000 in salary payments, most of which resulted from the company’s categorization of food truck managers as salaried employees instead of per-hour employees.

Muir wrote he believed food truck managers should be designated as salaried employees.

According to the department, Clover also compensated certain employees with regular instead of overtime payments when they worked 40-plus hour workweeks. Muir attributed these mistakes to occasional errors in the payroll person’s calculations.

The department further concluded Clover improperly deducted from its employee salaries. Muir wrote these deductions resulted from people taking vacations outside their paid time off.

Muir added he felt “fantastic” about most of the settlement.

“How can I be mad about paying any employee I love more money?” he wrote.

But he took issue with how the department handled the investigation.

“How can we have a system where small business owners are trying to follow every law but still can’t get it right?” Muir wrote. “And if something happens that was completely unintentional and you’re willing to fix it should you be punished?”

A spokesperson for Muir declined to comment and pointed to Muir’s blog post. Department of Labor spokesman Ted Fitzgerald also declined to comment and referenced the department’s earlier press release.

“The resolution of this case puts these wages into the hands of those who earned them, and demonstrates how our enforcement levels the playing field for law-abiding employers,” the release reads. “We encourage employers to use the tools and resources the Wage and Hour Division provides, and to reach out to us for assistance to avoid violations and operate in compliance with the law.”

—Staff writer Truelian Lee can be reached at truelian.lee@thecrimson.com. Follow her on Twitter @truelian_lee.