The money was taken from St Mary's Church and Christ Church in Ware and was thought to be around £500.
Every year churches across the country are asked to sell poppies as part of The Royal British Legion's fundraising campaign in the run up to Remembrance Sunday.
The boxes were taken during Sunday services on November 16.
Chairman of the Ware British Legion, George Rist, told the Hertfordshire Mercury: "What is it that gives these know-nothings the God-given right to walk into a church and steal money that is going towards helping the poor girls and boys coming back from war-torn countries?
"If perchance they are caught, what will they get? A slap on the hand and be told not to do it again?
"That money could buy two, maybe three wheelchairs."
Police are appealing for information.