After his brief professional playing stint, Bakich embarked upon his coaching career as a volunteer assistant at Clemson University in 2002. He worked as a hitting coach, and with both infielders and outfielders. Clemson advanced to the College World Series that season. Bakich then moved to Vanderbilt University in 2003 to become the school's recruiting coordinator, hitting coach, and outfield instructor. Collegiate Baseball ranked Bakich's first recruiting class the 24th best in the nation. In 2004, Vanderbilt increased its batting average from.258 the previous season to.304, the largest jump in school history. Vanderbilt brought in the No. 1 ranked recruiting class in 2005. Baseball America ranked the 2006 recruiting class 25th, and the 2007 class 12th. In 2008, the Commodores secured the No. 2 class. Each year of Bakich's seven-year tenure saw a top-25 ranked recruiting class.
In June 2009, the University of Maryland hired Bakich to replace former nine-year head coach Terry Rupp. Bakich sought to rebuild the program and eventually achieve regular appearances in the NCAA tournament, an event Maryland had not qualified for since 1971. His long-term strategy focused on recruiting, player development, and improving facilities. By September, Bakich had secured eleven commitments in the 2010 recruiting class and one in the 2011 class. He stated his plan to build a "recruiting wall" around the state to keep local talent at home. Bakich said, "Patience is not a virtue of mine. We don't have any time for that shit." Maryland finished its first season under Bakich with a 17–39 mark and 5–25 in the Atlantic Coast Conference. The Terrapins matched the worst finish in program history. Bakich said, "I know it sounds odd, but wins and losses have never been important to me. I wanted to change the attitude of this team first and foremost, and you can already see that happening. Our seniors have done a great job of leading this team, and the transformation has already been made." The 2011 recruiting class was described as one of the best in school history. Bakich resigned as Maryland's head baseball coach on June 27, 2012, in order to pursue his new head coaching career for the Michigan Wolverines baseball team.
On June 27, 2012, Bakich was named the 19th coach in the history of Michigan Wolverines baseball. On the same day of Bakich's hire, Bakich made his first public press conference as head coach of Michigan. Bakich was most noted for his quote, "We want to catch that softball program" meaning Michigan's softball program, and showed great praise for head Michigan Softball coach Carol Hutchins. Erik Bakich made many assurances that Michigan baseball will be back to winning championships at a consistent rate, not just every once in a while. Bakich also talked a lot about pitching and defense for Michigan, and bringing in the best recruits locally, regionally, and nationally. On May 24, 2015, Michigan defeated Maryland 4–3 in the Big Ten Conference Tournament championship game, securing a bid to the NCAA Tournamentfor the first time since 2008. During the 2019 season, Bakich led the Wolverines to a 50–22 record, including a 16–7 Big Ten Conference record, as they advanced to the College World Series for the first time since 1984. On June 15, 2019, Bakich was named the NCBWA National Coach of the Year. Later that year, Bakich received the 2019 Skip Bertman Award.
Head coaching record
Below is a table of Bakich's yearly records as an NCAA head baseball coach.
