Thun have sacked coach Urs Schönenberger as the club's fairytale season, which began with qualification for Uefa's Champions League, turns into a nightmare.
The move comes a day after the town's residents voted against ambitious plans for a new stadium.
Thun made an unexpected entry into Europe's elite club competition, which catapulted the small town, near the capital Bern, onto the football map.
But celebrations of Thun's achievements were cut short first by the club's elimination from the Champions League in November, by Sunday's vote and now by Schönenberger's departure.
"Schönenberger has had a lot of success here, but there have been problems with the team and there wasn't enough belief any more," said club president Kurt Weder.
Assistant coach Adrian Kunz has taken charge of the team three days before they make their Uefa Cup debut against German side Hamburg. Thun progressed to the Uefa Cup competition by virtue of finishing third in their Champions League group.
Eight years ago Thun were languishing in the Swiss third division, but the minnows battled their way through the ranks to become only the third Swiss team behind Grasshoppers of Zurich and Basel to take on the might of Europe.
The honour delighted the residents of Thun who flocked to the matches in unprecedented numbers and held a civic reception for the side when they completed their Champions League adventure.
Last year, Thun Mayor Hans-Ueli von Allmen revealed the impact the football stars have had on the town.
"Thun has profited a great deal from the accomplishments of the team," he told swissinfo. "The effect this is having on our image is priceless.
"I have recently spoken to people from South America, Africa and Arabian countries about our football success. It seems the whole world now knows about Thun," he added.
Thun were also nominated as Team of the Year in the 2005 Swiss Sports Awards, narrowly losing out to the national team which had qualified for the World Cup.
On top of the prestige and plaudits also came a substantial pot of prize money for a new 10,000 capacity stadium costing about SFr55 million ($42 million). But Thun voters clearly voted against this at the weekend.
Schönenberger took up position in January last year and managed to guide the club to second place in the Swiss top division. Victories against Ukranian side Dynamo Kiev and Malmö of Sweden then ensured qualification to the final stages of the Champions League, the first time Thun had reached such dizzy heights in their 107-year history.
swissinfo, Matthew Allen
FC Thun were founded in 1898 and played amateur third division football until the mid-1990s.
In 2002 they were promoted to the top flight of Swiss football.
The club runs on an annual budget of SFr5 million.
Thun has a population of 41,000.
FC Thun were only the third club to reach the final stages of Europe's premiere club competition behind Grasshoppers of Zurich and Basel.
Thun were drawn in a group comprising London giants Arsenal, Ajax of Amsterdam and FC Prague from the Czech Republic. Thun finished third in the group, which meant elimination from the Champions League, but qualification for the Uefa Cup.
This season is the first time in the club's history that they have qualified for either prestigious tournament. They are still in the Uefa Cup and play German side Hamburg on Thursday in Bern.
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