The Upper West Side store pulled the advertisement and apologized for any offense caused by the sign after customers complained, WNBC-TV, New York, reported Friday.
The sign, created by a store artist, was removed "once it was brought to our attention by a shopper that it may be perceived as offensive," a Whole Foods spokesman said.
"There was no disrespect meant at all," the spokesman said.
Customers were split on whether there were racist connotations to the sign.
"There are certain things that have been used to put down black people," Woody Henderson told WNBC.
"Even if he's not the president, you're going to have an African-American promoting the sale of chicken? They can do better than that," Jason Nunez said.
However, some said they did not see the sign as offensive.
"Obviously it looks like the president but I don't think it's racist," Joseph Joshua said to the television station.