The Louth Thirteen Plus Project came in second place to win £300 and Lincolnshire Wolds RDA came third to collect £200.
The money presentations follow after the two-week-long public vote where shoppers were asked to decide who they wanted to receive the biggest share of £1,000.
Claire Corn, manager of the Louth N&P branch, said: “We had a brilliant response to the campaign from our members, local shoppers and residents, but of course the real winners here are the charities – all of whom do a fantastic job of providing invaluable support in our local community.
“Each and every vote helped secure pounds for the charities and it felt right that the decision to split the money was put in the hands of our members and local people.
“I can’t thank everyone enough for coming in to our branch during the voting period to make their vote count – I’m sure the money will make a real difference locally.”
The Charity Choices campaign was supported by Yorkshire Building Society Charitable Foundation, which is funded by the Small Change, Big Difference® scheme where members donate the pennies from the interest they receive on their accounts, just once a year, to help charities and good causes in their communities. N&P is part of Yorkshire Building Society.