By the mid-2000s, the college was having financial issues and failing to meet "financial responsibility standards" of the United States Department of Education, a measure of economic viability. In 2009, Daniel Webster College received a score of just 0.5 out of 3 on that scale, with 1.5 considered passing.

Faced with the prospect of losing educational accreditation and federal funding, both of which would have forced the school to close, it was acquired by ITT Educational Services, Inc., the parent company of the ITT Technical Institutes in June 2009, and subsequently became a for-profit institution.

“The Bachelor of Science degree program in Aviation Flight Operations will be phased out over the next several years as the students who are currently enrolled in the program are allowed the opportunity to graduate within the normal timeframe for completion. Effective immediately, no new classes will be started in this program” Daniel Webster College.

Daniel Webster College currently holds a Federal Aviation Administration (FAA) Air Agency Certificate which is as an approved pilot school. The school operates flight instructional courses under Part 141 and Part 61 of the Federal Aviation Regulations.

Students completing these courses could earn pilot certificates and ratings issued by the FAA; commercial pilot certificate, with instrument and multi-engine rating. Students also had the option for preparation for a Flight Instructor Certificate.