Mum-of-six Comfort Konadu got the cash when she asked for a £9 refund.
Instead of notifying Mencap staff of their error when she found out, she transferred cash to the accounts of family and friends in a flurry, it was said.
The charity recouped two-thirds of the £90,047 — partly by freezing her account — but £31,000 remains outstanding.
It dismissed two staff over the blunder at the shop in Openshaw, Manchester, and is expected to be liable as the loss was caused by human error.
Konadu will face a Proceeds of Crime hearing where an attempt will be made to retrieve the £31,000 — which represents 18 months’ profit for the shop.
It was not known what the money was spent on.
Max Saffman, defending, said Konadu sent some of the cash to Ghana, her homeland.
He told Manchester crown court: “Until this windfall she was leading a very, very modest lifestyle and she is a hard-working lady. Temptation got the better of her.”
“This was a serious amount of money and a serious offence.”
Konadu admitted theft and was jailed for 15 months, suspended for two years.