Flowers, (pictured) who stepped down from the Co-op Bank six months previously after concerns over expenses, was arrested in November last year after newspaper allegations he was involved in a drug deal.
He has been charged with two counts of possession of a class A drug and one count of possession of a class C drug.
A second man has also been charged with offering to supply drugs.
The charges against Mr Flowers relate to possession of cocaine, methamphetamine and ketamine.
Flowers, accompanied by two minders, fought through waiting photographers and TV crews as he arrived at Stainbeck Police station in Leeds earlier.
His solicitor Andrew Hollas told those gathered outside his client would make a full statement after an appearance at Leeds Magistrates’ Court next month.
The troubled Co-operative Bank moves from one hiatus to another following worrying financial results last week and as Lord Myners announced his shock resignation from the board of the Co-op Group under a week ago, leaving the mutual in the middle of a review into its future.
The former Labour City minister has quit as the senior independent director of the troubled group less than two months after the resignation of chief executive Euan Sutherland.
In October, the embattled Co-operative Group announced a restructure which would give it a 30% stake in the struggling Co-op Bank, with 70% handed to hedge funds and other creditors.
