Sharon Meijland, who runs the Rainbow Cafe in Cambridge, made the move earlier this week after it emerged the currency contains tallow, which is used in the production process.
The businesswoman claims her customers have been supportive, but she has been left shocked and frightened by some of the "hatred" from other people.
She said: "Our own customers who are actually in the restaurant in Cambridge have been very favourable, but on Facebook there's been a good deal of charming comments such as 'I hope this comes back to bite you in the a**"'.
The 66-year-old said she believes some people are reacting in such a way "because I made a stand" and said she had been wrongly accused of seeking publicity for the cafe.
Fury among vegetarians, vegans and members of religious groups erupted once it was confirmed by the Bank of England the polymer notes contain animal fat.
Ms Meijland said she spoke with staff and they decided they could not justify handling the notes, which came into circulation in September.
"We all said we felt very uneasy about handling it (the note). We thought the only way round this is to just not accept them."
Vowing to stick with the decision, she added: "I am shocked and frightened at my age to get such hatred (online)."
A petition against the use of the note has been started, and so far more than 125,000 people have signed it, including Ms Meijland.
The Bank of England said it is "aware of some people's concerns" and is looking at "potential solutions".
It said it was treating the concerns with the "utmost respect" and was in discussion with its supplier, Innovia.