Mr Flowers was arrested in November following newspaper allegations he was involved in a drug deal. He had stepped down from the Co-op six months earlier over concerns about his expenses.
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.
'Hounded'Accompanied by two minders, Mr Flowers 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 following his appearance at Leeds Magistrates' Court next month.
"He has been hounded for six months by certain elements of the press and they have included many allegations within their papers that have been completely without foundation," Mr Hollas added.
Claire Stevens from the Crown Prosecution Service said Yorkshire and Humberside's Complex Case Unit had "carefully considered a file of evidence gathered by West Yorkshire Police" in relation to the alleged offences.
"Following a review of the evidence, I have concluded that there is sufficient evidence and it is in the public interest to charge Paul Flowers with possession of Class A and Class C drugs relating to an incident on 9 November 2013," she added.
The second man, Gavin Woroniuk, is accused of offering to supply cocaine, methamphetamine, cannabis and ketamine, the CPS said.
Mr Woroniuk also faces a charge of possession of criminal property.
The former bank chairman appeared before MPs on 6 November last year The drugs allegations put Mr Flowers at the centre of a political row as the Conservatives highlighted his connections to the Labour Party.
Chancellor George Osborne launched an inquiry into how he was deemed suitable to chair the bank.
The Methodist preacher had previously served as a Labour councillor in Bradford and on an informal board advising Ed Miliband on banking.
But his appearance before the Treasury Select Committee in November last year was widely criticised.
It has also since emerged that Mr Flowers left Lifeline, a drugs charity based in Manchester, after allegations about his expense claims.
