Mr Niccol joined Starbucks as its chief executive last year, on the heels of a six-year stint at at the helm of Chipotle Mexican Grill. During his tenure there, the fast-casual burrito chain nearly doubled its sales.
The latest store closures and layoffs at Starbucks are part of Mr Niccol's wide-ranging turnaround strategy in his first year at the company, as the chain tries to lure back dissatisfied customers. His efforts have included remodelling stores to revamp seating and bringing back self-service condiment bars.
The company is also facing a unionisation campaign among baristas at its US stores.
Workers United - which is part of the Service Employees International Union and said it represents workers at more than 600 of Starbucks' company-owned US stores - is fighting for a contract agreement with the company.
The union has voiced concerns about under-staffing at stores and overwhelmed baristas, among other issues.
In response to the company's restructuring announcement on Thursday, Workers United said it was a sign that "things are only going backwards at Starbucks under Brian Niccol's leadership".
"Yet again, we're experiencing new policies and major decisions being made with zero barista input," the union said in a statement, adding that it was sending a formal request for information to Starbucks about the planned closures.