The MTA’s subway and bus chief resigned today — under pressure from the MTA’s new CEO — with a $300,000 severance package

Howard Roberts left after weeks of speculation that he would step aside as the agency’s new CEO settled in to the job.

Roberts’s departure, who was at the helm of New York City Transit for more than two years, could signal the beginning of a house-cleaning by new MTA Chairman Jay Walder, sources said.

“Howard deserves credit for his hard work leading NYC Transit over the last two and one half years,” Walder said in a statement. “He will remain in his position through the end of November. I intend to name a replacement in short order.”

Roberts recently oversaw a wide-scale rehab of how the subway system is managed, by introducing bosses for each line.

But straphangers – and rider advocates on the MTA board – have also expressed frustration with the scheduling of repair work, which has recently clogged up weekend subway service.

“Although saddled with budget cuts and disruptions caused by needed repair work, he put managers in charge of each line and pushed to provide faster bus service,” said Gene Russianoff, of the Straphangers Campaign. “The subways and buses can drive New Yorkers nuts, but Howard Roberts worked hard for a saner system.”