NEW YORK — New Yorkers may soon be able to count calories burned and miles traveled while pedaling Citi Bikes, the popular bicycle-sharing program with a troubled history that is undergoing a major overhaul under new leadership.

The new CEO of the Brooklyn-based company that owns Citi Bike says a revamped smartphone app soon will offer such detailed fitness stats and allow people to make real-time reports of such issues as flat tires or broken seats.

Jay Walder, a mass transit veteran who used to run the city’s Metropolitan Transportation Authority, envisions the bikes becoming a seamless part of the city’s transportation network, with plans in the works to incorporate docking stations into architectural design plans for massive new development projects.

“We are still defining how bike share should fit into the urban fabric of the city,” said Walder, who became chief executive officer of Motivate, the company that owns Citi Bike, several months ago. “Maybe it could be inside of businesses. Maybe it could be inside of buildings. Maybe it could be built into the environment.”

Launched in May 2013 to much fanfare, the wildly popular public bicycles have endured a bumpy ride. Superstorm Sandy swamped and damaged a fleet of bicycles in Brooklyn in 2012 and delayed the program’s debut. Bikes got stuck at docking stations and were poorly maintained. The app wasn’t reliable. People complained of a dearth of bikes in the most high-trafficked areas of the city.

Alta Bicycle Share, its parent company, was nearly bankrupt when it was bought by a group of investors, then rebranded as Motivate.