The team at Cafe Nicole's in Morley have spent the past month raising funds for Cancer Research, inspired in part by the death of the owner's step sister a few years ago.
But as the first staff member arrived today, they found the door to the cafe in Annie Street had been smashed open.
Burglars had taken the till and a Cancer Research charity box brimming with donations from generous customers.
Nicola Copley, of Cafe Nicole's, said: "We've lost all of the morning trade, but the main thing is the staff who opened up weren't hurt."
She said that when the burglars prised opened the stolen till, they would find very little inside.
"We don't leave large amounts of money in there," she said.
"What we're most upset about is them taking money from a charity that's so close to our hearts. It's just disgusting."
The popular cafe, which won the Yorkshire Evening Post's Cafe of the Year competition back in April, was able to reopen by around 11am when forensics officers finished their work.
Tomorrow its community spirited staff had been due to 'gunge' one of the team after inviting regular customers to cast votes in return for donations to the cancer charity.
Now they plan to delay the fundraising stunt in the hope of rebuilding the stolen collection.
West Yorkshire Police said the burglary had been found to have taken place shortly before 1.50am.
A spokesman said they had been alerted at 7.10am and officers were continuing to make enquiries.
Anyone who witnessed anything suspicious or who has any information is asked to contact officers via 101, quoting crime number 13170506157.