Glenn Mack Jr., 24, had been working at the Philadelphia store for about two years and, said his lawyer, loved his job. In the fall of 2010, he made a vacation request to take 18 days off, 2½ months before his time off was to start. Whole Foods requires two-week's notice for time off.
Mack's plan was to go to Saudi Arabia and make a pilgrimage to Mecca, the holiest city in Islam.
"When [Mack's supervisor] discovered [Mack] was going to Mecca for his pilgrimage, that's when things started to change," said Mack's attorney, Amara Chaudhry, the civil rights director at the Philadelphia chapter of the Council on American-Islamic Relations. "He was told his job would not be guaranteed upon his return."
In a complaint filed with the U.S. Equal Employment Opportunity Commission, Mack claimed his supervisor "had previously been heard making Islamaphobic comments," according to Chaudhry, and Mack said he was given a difficult ultimatum.
"His supervisor apparently said to him, 'You can choose. It's either your job or your religion,'" Chaudhry said.
Mack chose his religion and made his pilgrimage.
When he returned to Whole Foods, he was demoted from full-time to part-time status, and he said his co-workers treated him differently.
"People started to interfere with him while he was praying," Chaudhry said. "He had a secluded area away from customers where he would go during breaks to pray." Eventually, Mack resorted to praying outside next to a Dumpster.
Mack complained to human resources and was restored to full-time status but was fired about three months later. Chaudhry said he was fired "allegedly for attendance reasons," but he had not received any warning or notification before Whole Foods ended his employment.
"[Mack] had been with the company since 2008 and had actually received many accolades," Chaudhry said. "He had been an exemplary employee by all accounts."
Whole Foods would not comment on Mack's case specifically, but released the following statement from Whole Foods spokeswoman Robin Rehrield:
"While we don't give out details about current or former team members, we can say that we deny such allegations. We value and celebrate diversity, and we have a zero-tolerance discrimination policy," as reported in the Philadelphia Inquirer.
Mack's EEOC complaint has been pending since March 2011.
"That doesn't read to me as though the other side is interested," Chaudhry said.
This is the second time in recent months that Whole Foods has been at the center of a religious-fueled controversy. In August, the company was criticized for directing a marketing campaign at Muslims during the holy month of Ramadan and then taking it back.
While many celebrated Whole Foods' decision to recognize and celebrate the beliefs and customs of its Muslim customers, some anti-Muslim bloggers accused the grocery chain of "Islamo-pandering." But the real trouble for the company came when the Houston press obtained an internal email suggesting that some of the stores should downplay any mention of Ramadan, in light of the criticism.
Mack has been disappointed and hurt by the conduct at his store, but he hopes to return to Whole Foods.
"He wants his job back," Chaudhry said. "He loves Whole Foods as a company and wants to make his career there." Mack had previously worked at Whole Foods stores in New Jersey, and Georgia and had been recruited to work at the Philadelphia store.
Through his suit, Mack is seeking immediate reinstatement of his job, monetary damages for his losses related to the termination of his employment and mandatory training for managers and staff on "relevant and applicable anti-discriminatory laws, but also culture and diversity training," Chaudhry said.
"We actually want to remind employers of their obligations under anti-discriminatory laws," Chaudhry said. "We want to make employers and employees aware that, not only do these laws exist, but there are people willing to stand up and enforce these laws."
Additional reporting by ABC News' Anne-Marie Dorning.