"Brian is a proven world-class executive, who will bring fresh energy and leadership to drive excellence across every aspect of our business", said Ells, who will become Chipotle's executive chairman, in a statement.
Ells added that the expertise of Niccol in restaurant operations, branding and digital technologies makes him the flawless fit for the chain as it seeks to enhance the customer experience, increase sales growth, and make the brand much more relevant.
Niccol joined Taco Bell in 2011, taking the helm four years later.
The Denver-based company has struggled to recover from a foodborne illness outbreak in 2015 that included 55 cases of E. coli O26 across 11 states followed by a norovirus outbreak at a Boston-based restaurant that reportedly sickened 80 individuals.
Niccol, 43 and head of Yum Brand's Taco Bell since 2015, on March 5 will replace Chipotle founder Steve Ells, who built the chain on the idea that food could be both healthy and fast but failed to nail the operational prowess needed to guide it through several health scares.
Still, Chipotle can not simply repeat the Taco Bell formula with better ingredients.
For investors - who saw Chipotle's stock jump almost 12% in after hours trading yesterday - choosing Niccol is "certainly a safer, more reassuring choice", University of Denver assistant business professor Paul Seaborn tells The Denver Post's Joe Rubino.
"Will Chipotle somehow mimic the Taco Bell menu, market positions and brand flavor?"
No doubt, Chipotle is looking for Niccol's magic marketing touch to boost the Denver-based brand during challenging times.
After the news of change in the leadership at Chipotle, its shares surged over 11% in NY.
Last year, Chipotle also suffered a security breach involving customer payment data, while new menu additions did not entice diners as it had hoped. She will also continue the brand's strong partnership with its franchisees to deliver world-class operations.
Since then, Taco Bell has been unstoppable when it comes to getting its message before experience-driven millennials.
Succeeding him at Taco Bell are Julie Felss Masino, president of Taco Bell North America, and Liz Williams, president of Taco Bell International, who will jointly assume leadership of the Taco Bell division in their respective roles, reporting to Yum!