Tony Winters has complained to Trading Standards after the shop tried to charge him 25p for a sachet of tomato ketchup, claiming it was "racial discrimination".
Mr Winters was with his fiancee and friend when they went to the Gold Sea chippy in Ferry Road.
The father of five, originally from Glasgow but who has lived in Edinburgh for 18 years, said it was "morally wrong" for the shop to offer one sauce free while charging for the other. He said he felt "racially persecuted".
Mr Winters said: "I couldn't believe it. Every chip shop I know gives ketchup free. Just because we come from the west and tend to like ketchup instead of brown sauce. It's clear they're discriminating and I don't think it's right.
"I'm feeling racially persecuted because of a condiment."
However, Gold Sea owner Paul Crolla said: "People in Edinburgh want salt and sauce on fish and chips. That's the tradition. If you go to Glasgow it's salt and vinegar.
"It's not just like we offer two sauces, we do it so customers have a choice. For this guy to suggest it is discriminatory takes the biscuit."
Trading Standards said it was up to individual traders to decide if they wanted to charge for sauces and said there was no case to answer.