The deal with poultry producer Wiesenhof might solve the club's financial problems, but it has ruffled the feathers of many fans.
Wiesenhof was the subject of a documentary last summer which showed extensive animal cruelty, terrible hygiene and rock bottom wages paid to workers. Although the north German firm said the documentary was unfair, it has not been able to shake off the criticism.
Animal protection group Peta has also criticised the firm, saying it had found dead animals lying among live ones and many ducks that were too weak to stand up.
A further investigation by Die Welt newspaper also exposed serious problems, with one former employee talking about meat being processed and sold even though it had fallen on the floor.
Wiesenhof is owned by PHW Gruppe, which says it slaughters 4.5 million chickens a week in Germany, producing more than €2 billion a year in turnover.
McDonalds said in March it was not going to use any Wiesenhof products until the hygiene problems were resolved to its satisfaction.
The report in Germany's biggest newspaper Bild that Werder Bermen was going to put Weisenhof's logo on its kit provoked a storm of protest.
Although the club has not confirmed the report, its website was filled with negative comments, Die Welt reported, while a Facebook page has been set up by those against the idea.