An Edeka store in the southwest German town of Ruelzheim has piloted the technology since November, cutting out on time otherwise wasted scrabbling for coins or cards.
The company plans to equip its stores across the region with the ground-breaking technology.
"All customers need do is register once with their identity card and bank details, then they can shop straight away," said store manager Roland Fitterer.
The scanner compares the shopper's fingerprint with those stored in its database along with account details.
Edeka bosses said they were confident the system could not be abused.
The chance of two people having the same fingerprint is about one in 220 million.