Chipotle Mexican Grill's Steve Ells is stepping down as CEO and it could be just what the company needs to finally cement a solid turnaround.

The burrito chain announced Wednesday that it's begun to search for a new chief executive, sending shares of the company up more than 5 percent.

Jeremy Scott, senior research analyst at Mizuho Securities, called the decision "unexpected," particularly after the company recently streamlined the CEO position from two co-CEOs, a post Ells had shared with Monty Moran.

"But [it] is an absolutely critical, important next chapter for Chipotle, which has been struggling to recover sales under Ells," Scott wrote in a research note Wednesday.

The Colorado-based restaurant chain has been testing initiatives to lure customers back ever since it faced a slew of foodborne illness outbreaks in 2015. However, its efforts have been overshadowed by a number of food safety incidents and a payment system breach.

"The decision of Steve Ells to step down as CEO is the inevitable consequence of Chipotle's inability to get to grips with its various problems," Neil Saunders, managing director of GlobalData, told CNBC via email. "Under his leadership, the chain has stumbled from one crisis to the next and has failed to reignite the growth that it once enjoyed."

"Steve Ells' success in founding and growing Chipotle is not in question, but his ability to run a larger publicly owned company and to guide it through choppy waters was," Saunders said. "While not entirely his fault, the continued lack of momentum concerned investors and raised questions about his leadership and his vision for the group."

As of Tuesday's market close, Chipotle shares have fallen more than 24 percent this year.