The free one hour parking scheme will end at the end of May, and motorists will have to pay from the off from June 1.
The Boston Borough Council scheme was originally for two-and-a-half hours and was brought in at the end of the first lockdown last year.
It was later reduced to one hour.
A spokesperson for Boston Council said: “The council has been really pleased to be able to offer this initiative for so long, in order to support local businesses for whom the last year has been so very tough.
“From the June 1, shoppers and visitors will need to purchase car parking tickets for their desired length of stay from the ticket machines in all of our car parks, or alternatively, use the MiPermit app in our off-street car parks if you prefer to pay by phone.
“All day parking is available for as little as £2.”
The Council’s car parking charges can be found in its car parking guide here.