David Spencer is alleged to have stolen money from Holy Trinity Church and St Andrews Church in early July.
He's also accused of taking a collection tin from All Hallows Vicarage.
The 46-year-old, who has no fixed address, appeared at Wimbledon Magistrates Court.
He has been charged with six offences of burglary.
Police had released an image of a man they wanted to speak to in connection with the alleged thefts.
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