Dee worked for the team from 1995-2002. He was part of the front-office group that followed former team president and CEO Larry Lucchino to the Red Sox.
"It's a dream come true," Dee said on a conference call with reporters on Wednesday. "I'm anxious to get started on the journey ahead. I never got baseball out of my blood."
Dee was the Padres' executive vice president of business affairs his final three years in San Diego. All told, he's spent 15 years working in baseball.
Dee previously was the CEO of the Miami Dolphins and Sun Life Stadium, a position he took in 2009.
"Mike's enthusiasm, his love for San Diego, his love of the Padres. ... He's going to be an extraordinary leader for the new ownership group," said Dan Novak, vice president of global marketing, public relations and communications for Qualcomm.
Dee rejoins the Padres with a long-standing relationship with club executive chairman Ron Fowler. Dee also worked for three years with San Diego general manager Josh Byrnes, who worked in Boston's front office during Dee's tenure with the Red Sox.
"I've known Mike for 18 years, and from the first time I met him, I was impressed with his energy and his creativity," Fowler said. "Bottom line, from my perspective, Mike Dee is a winner."
Dee was hired to replace Tom Garfinkel, who resigned as the team's president and CEO on July 9 after holding the post since 2009.
The Padres moved quickly and decisively in finding Garfinkel's replacement. The search led them to Dee, who has known Fowler for the past 18 years.
"Mike was the top person on our list," said Padres lead investor Peter Seidler. "The gap between Mike and No. 2 was big."
Scott Marshall, the Padres' vice president of concessions and retail, first got to know and work with Dee when he was with Centerplate, which is one of the largest hospitality companies in the world.
"I honestly believe there's no better candidate than Mike Dee," Marshall said. "His energy and passion are unmatched. He's committed to three things: to a championship, fan engagement and community.
"When Mike came here in 1995, he got to our market, which is dynamic and unique, very quickly. He's an incredible innovator. His attention to detail is phenomenal."
Dee's previous tenure featured the planting of the palm trees that lined the outfield at Qualcomm Stadium, incorporating different logos and having unique promotions that helped attract crowds in excess of 50,000, particularly in 1996, into the Mission Valley ballpark.
"I think what makes this region special is the people," Dee said. "The Padres to me were such a unifying force for the region. That's what I'm signing up for.
"This is an opportunity to restore the Padres to that unifying force. I was part of a great management team back in the '90s. The entire city and region was hopping. That's what we want to restore."
Dee also spearheaded efforts in developing strong ties and programs to the Hispanic community in San Diego, Tijuana and Baja California. It was during that time the team played regular-season games in Mexico in 1996 and '99.
Dee played an integral role in helping generate public and corporate support that led to the approval and construction of the team's downtown ballpark, Petco Park, which opened before the 2004 season.
Novak first worked with Dee when Novak was the vice president and general manager of 4SD (Channel 4 in San Diego), the regional sports network that had the Padres as its centerpiece.
"We worked literally daily on a variety of fronts ... like how to present the Padres brand organization to the fan base," Novak said. "We worked very closely on what kinds of content we were going to develop and how we were going to position the team in the best way possible to reach our fan base."
4SD produced Padres games that were broadcast on KUSI from 1997-2003. In 2001, the team inked a 10-year deal with the station. 4SD was the exclusive broadcast partner for the Padres from 1997-2011.
That relationship blossomed, Novak said, in part because of the efforts of Dee.
"Mike is the best sports executive I've ever dealt with," Novak said. "We were able to collaborate and really focus on a shared vision for what we were trying to create; what's the best thing to do for the customer or the fan. From the parking lot to the concessions, how do we tell that story, how do we make sure fans get great value?"
With the Red Sox, Dee was promoted to chief operating officer in 2004 and was instrumental in Boston's growing attendance and revenue.
Dee oversaw business operations, including the implementation of the popular Green Monster Seats, as well as directing the expansion of the team's business and real-estate interests during an eight-year renovation project of Fenway Park and the surrounding neighborhood.
Dee also served as president of Fenway Sports Group, a wholly owned subsidiary of New England Sports Ventures, the parent company of the Red Sox that was charged with diversifying the business interests of the team outside of baseball, including the acquisition of 50 percent of NASCAR's Roush Racing.
But now it's back to baseball, a move that Dee wouldn't have predicted a year ago, six months ago, let alone six weeks ago. Dee believes he steps into a good situation with the new ownership group that's been on the job for a year.
"The foundation starts at the top … the ownership group that Ron and Peter -- that was a giant quantum leap for that restoration," Dee said. "You've got to have strong ownership.
"I believe those core building blocks are in place," Dee said. "All the pieces are in place. We've just got to be smart about the way we want to go about things."
Now he's back to San Diego. Marshall, for one, is looking forward to what will follow.