Her personal work for Pruitt raised red flags among ethics experts.
A second top Pruitt aide, senior adviser Sarah Greenwalt, informed colleagues on Wednesday that she also is leaving the EPA and returning to Oklahoma for work at a state agency.
Calls for Pruitt himself to resign has continued to mount amid a dizzying number of ethical scandals involving his dubious oversight of the EPA and unprecedented spending on taxpayer-funded travel, security and accommodation.
"Look, my wife is an entrepreneur herself, I love, she loves, we love Chick-fil-A as a franchise of faith and it's one of the best in the country and that's something we were very excited about and we need more of them in Tulsa and we need more of them across the country", Pruitt said by way of explanation on Thursday.
One half of the departing duo, Millan Hupp, had a turn in the headlines a few days ago when congressional Democrats released testimony in which she discussed Pruitt's pursuit of a used Trump Hotel mattress - one in a series of personal errands it's been alleged he charged or allowed Hupp to lead.More news: Sessions: DOJ Is 'Pleased' At Supreme Court's 'Masterpiece Cakeshop' Ruling
Jahan Wilcox, a spokesman for the E.P.A., did not comment on the departure of Ms. Greenwalt.
Pruitt previous year directed his EPA scheduler to reach out to a top executive at Chick-fil-A to inquire about a "business opportunity".
"Sarah has been a tremendous leader within the agency, overseeing the start of the WOTUS rewrite as well as playing a vital role in our global relations", Pruitt said in a statement. Federal rules bar public officials from receiving gifts from subordinates, including unpaid services, and from using their office for private gain. Pruitt, in a television interview Wednesday, didn't say whether he thought he had acted inappropriately.
Environmental Protection Agency head Scott Pruitt already faces at least 12 federal inquiries from the EPA's Inspector General, Government Accountability Office, and House Oversight committee.
Pruitt actually suggests it's only a story because he's making big changes and "with great change comes significant opposition".