The mayor of Roubaix, in northern France, said the halal menu constituted â€œdiscriminationâ€ against non-Muslims.
The Roubaix branch is one of several restaurants at which the chain, Quick, took non-halal products and pork off the menu in November.
The move has triggered the latest row over Franceâ€™s Muslim minority.
Several deputies from French President Nicolas Sarkozyâ€™s conservative UMP party have condemned the move, while Marine Le Pen, a vice-president of the far-right National Front, warned of â€œIslamisationâ€.
Their comments came ahead of regional elections in France next month, and against the backdrop of a debate over French national identity launched by Mr Sarkozyâ€™s government.
â€˜Going too farâ€™
In Roubaix, Mayor Rene Vandierendonck, a socialist, called for a boycott of the Quick branch, and the town council has filed a complaint for discrimination with a regional court in Lille.
â€œIâ€™m not bothered by the fact that there is a halal menu,â€ Mr Vandierendonck said.
â€œBut this is going too far because it is the only menu on offer and it has become discrimination.â€
Quick decided to take a bacon hamburger off the menu at eight of its 350 branches, replacing it with a halal version that comes with smoked turkey.
It said the move was designed to test the â€œcommercial interest and technical feasibilityâ€ of introducing halal menus.
The Quick manager responsible for the Roubaix branch said there had been a slight increase in business after the introduction of halal menus and that he had not received complaints from customers, AFP news agency reported.
France is home to Europeâ€™s biggest Muslim minority, estimated at more than five million people.
Debate has recently focused on the Islamic veil, with a French parliamentary committee recommending a partial ban on women wearing Islamic face veils last month.