John Pepper, co-founder of Boston-based Boloco, has ended his 17-year tenure, officially stepping down from his position as chief executive officer of the company on Monday, October 7.

Pepper founded Boloco, which went under the name “The Wrap” until 2005, with Adam Liebman and Gregg Harris, in 1996. The very first location opened on Mass Ave. across from the Berklee College of Music in February 1997. Today, Boloco has 22 locations and expects over $27 million in annualized sales in 2014.

According to a letter issued to the Boloco team in mid-October, and supplied to BostInno by a Boloco team member with Pepper’s support, his resignation was the result of the termination of a deal between Boloco’s current ownership and its new investors. The $15 million deal went south at the eleventh hour because the two parties could not resolve their different views regarding control of the company.

Said Pepper:

I put my job on the line and issued an ultimatum to our Board and current ownership, with one of the options to accept my resignation “for good reason.” I walked the proverbial plank and sadly never got to get back on our boat. Our current owners accepted my resignation and rejected the deal.

Despite being forced to resign in such a manner, Pepper has nothing but high hopes for the future of Boloco. “A company like ours, in its current state and at its current size, can be and is a wonderful place to work and to thrive for most of you, for many years to come,” he said in the letter.

Throughout his time at the head of the Boloco franchise, the former CEO has developed some seriously succulent burritos. Serving his community was always Pepper’s primary priority, however. In an interview in 2011, Pepper told Forbes the Boloco philosophy is:

To be appealingly off-center (i.e. never boring!), to not take ourselves too seriously, and to strive for 100 percent honesty even when it hurts … While we absolutely love that our culture is one where we consistently go overboard to amaze our guests, to make up for mistakes, and generally shock and awe those who visit us, our main focus is on positively impacting the lives and future of our people.

Pepper is very vocal about the issue of giving workers higher wages and he has been enthusiastically involved with the Boston community through social media, as is evidenced by a quick glance at his Twitter account, @bolocoCEO.

“Social media allows us to bring our teams and our restaurants to life even for those who aren’t presently in one of our restaurants,” Pepper said in the Forbes interview.

During Hurricane Sandy, Pepper’s commitment and enthusiasm to staying open and serving his community  — a message he spread over social media — garnered him some severe backlash. Pepper’s response, circulated via email, was as compassionate as it gets:

For the record, we have allowed all team members who need or want to go home to do so … We stay open because we employ people on an hourly basis who rely on Boloco being open to pay their bills and care for their families. When we close, they make no money.

Though he admits this move “happened very quickly,” Pepper remains confident in the company he founded and its path toward future success. He even alluded to this move being a positive for Boloco’s greater good. “Trust me on this,” he said, “there exists, somewhere, a far more experienced CEO candidate with a fresh perspective who will lead a 22-unit restaurant chain like ours to solid ground and long-term prosperity, while maintaining our unique people-first culture.”

In the conclusion of his letter, which went out to “Team Boloco” with the subject line “Ch-ch-ch-changes,” Pepper offered this:

Boloco is full of so many incredibly talented, generous, good-hearted people. I leave my day-to-day role as CEO knowing that if we select the right leadership to go forward, a very promising future lies ahead for many of you who choose to continue believing in and relentlessly pushing for our purpose, mission and best possible performance.

No word yet on what Pepper has cooking for his next endeavor, but we will be eagerly waiting to see what one of Boston’s marquee entrepreneur serves up next.

As for his future with Boloco, he will be “supporting from the sidelines” – serving as owner, possible board member and chairman, and of course, “as a believer.”