An image of the trio appeared on an article called "how to become a congressman".
It appears a photo of a 2012 fundraising event had been turned into a cartoon, with all three being "whitewashed".
WikiHow said it should never have been on the site.
The website is an online community which provides guides on how to do things and often uses cartoons to illustrate its step-by-step points.
In a series of tweets, wikiHow tried to explain what happened.
It said: "Within minutes of the first tweet, a volunteer removed the image. We then started investigating how it got on wikiHow at all.
"We learned it was made three years ago by a team of illustrators who work as one. One person sketches, the other person colours. The sketcher sent the colourist a black and white sketch.
"The colourist wasn`t aware it was Obama and Beyonce. We don`t think the illustrator intentionally whitewashed here.
"This doesn`t excuse the fact that we hosted a terrible image on wikiHow and we needed more diversity on that article period.
"We`re talking with our illustrators to prevent recurrence and encourage diversity. Especially in positions of power."
The original photo of Beyonce, former US president Barack Obama and Jay Z was taken in 2012 at a fundraising event in New York.
WikiHow apologises for `whitewashing` Beyonce, Jay Z and Barack Obama
26 January 2017
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WikiHow says it`s "disgusted and ashamed" after posting a picture of Barack Obama, Beyonce and Jay Z which depicted them as white people.
