McGregor continued running as a student-athlete at the University of Michigan in the fall of 1995, majoring in English and competing in both cross country and track.

She was the first freshman and first Wolverine to complete the course at the conference championship meet, helping her team to third-place finish behind the champion Wisconsin Badgers.

[3] McGregor's sophomore cross country season was somewhat disappointing, as both she and all but one of her Wolverine teammates missed qualifying for the NCAA championship meet.

[4] During her junior cross country season in the fall of 1997, McGregor was named Big Ten Athlete of the Year after winning the individual title with a time of 17:14.

[15][16][17] During the 1999 outdoor track season, she won her final collegiate championship, winning the Big Ten title in the 5000-meter run with a time of 16:32.83.

[20][21] Following college, McGregor remained in Ann Arbor and continued training and competing under sponsorship from Adidas, transitioning from the shorter distance races to the 10000-meter run.

Over the next few years, McGregor competed in variety of distance races, performing well, and continuing to improve upon her personal best times in several running events.

Highlights during 2004 included a second-place finish at the U.S. Cross Country Championships (8000-meter distance),[22] as well as personal bests in both the 5000-meter and 10000-meter runs prior to the Olympic Trials.

[24] She competed in the event for the U.S. team at the IAAF World Championships in Athletics in Helsinki, Finland in August 2005, taking fourteenth place overall as the top U.S. finisher, with a personal best time of 31:21.20.

[26] In the spring of 2007, McGregor won the USATF 25 km championship, completing the River Bank Run in a time of 1:25:53 nearly three minutes ahead of the rest of the field.

Amy Yoder Begley made a furious charge at the end of the race, which met the standard and therefore qualified her for the team over McGregor.