The man was caught during a check last spring by federal alcohol administration employees of one of one of his catering operations, where untaxed foreign liquor was discovered.
This led to a further investigation by the Federal Customs Administration (FCA) who found the restaurateur had been illegally importing food a drink over a four-year period.
In the process he avoided paying 32,000 francs ($36,700) in import duties, customs officials from the local Schaffhausen office said in a news release.
The FCA would not say how many restaurants were involved in the smuggling car because of criminal proceedings still under way, the Tagblatt newspaper reported.
The accused man transported the food in his car usually crossing the eastern border of Switzerland from Vorarlberg in Austria.
The contraband included one ton of meat and meat products, 800 kilograms of dairy products, three tons of fruit and vegetables and three tons of fats and oils, the FCA said.
Customs said the case is not isolated, noting that a total of 36 criminal investigations have been launched into similar food smuggling operations since 2010 in Eastern Switzerland and the principality of Liechtenstein.
Spokesman Jürg Vögeli told Tagblatt the cases involved restaurants, food stalls and smaller grocery stores.
Import duties evaded in the cases totalled around 370,000 francs, the FCA said.
Food is generally cheaper in Austria and other countries in the eurozone than in Switzerland.
Customs officials said with the recent rise in the value of the franc to near parity with the euro cases of smuggling are expected to rise.