WASHINGTON — Two top aides resigned Wednesday from the Environmental Protection Agency as its administrator, Scott Pruitt, faced mounting allegations of misusing his authority, including by seeking a Chick-fil-A fast-food franchise for his wife.

Millan Hupp, Mr. Pruitt’s scheduler, and Sarah Greenwalt, a senior counsel to the administrator, have come under scrutiny in recent weeks in connection with Mr. Pruitt’s spending and ethics concerns.

Before joining the agency, both Ms. Hupp and Ms. Greenwalt worked for Mr. Pruitt in Oklahoma, where he served as attorney general. Both aides later received substantial raises at the E.P.A., bypassing the usual White House procedures. Mr. Pruitt told Congress he neither knew about nor approved of the raises, and he told lawmakers he reversed the raises when he learned about them.

The departures come as Mr. Pruitt faces fresh questions about his management decisions. On Monday, Democrats on the House Oversight Committee, which is conducting one of 12 investigations into his spending and ties to lobbyists, released a partial transcript of an interview with Ms. Hupp showing that Mr. Pruitt asked her to do personal errands for him, including apartment hunting and asking the Trump International Hotel if Mr. Pruitt could purchase a used mattress.