Some accounts that Anonymous members won access to had their messages and images changed to show the ISIS-Chan anime character. Groups tackling IS propaganda online are starting to use images of the young girl in connection with the group's name and slogans in an attempt to dilute the results people get when they search for information about the group.
The Anonymous action comes after UK Prime Minister David Cameron unveiled a strategy to help tackle the "poison" of extremism. The package of measures included demands that ISPs and net firms do more to remove extremist material and identify who posted it.
It is not clear how much effect the action by Anonymous and others is having on the work IS does to spread its message online. One study released earlier this year estimated that the group and its sympathisers control more than 90,000 Twitter accounts.
"There is definitely utility in shutting down accounts," said JM Berger, an analyst that did the study of IS' use of social media.
"It's not going to eliminate IS's presence online, but it helps limit their ability to accomplish their goals, particularly with respect to spreading its propaganda outside of its core audience," he said.
"It also wastes their time and requires ISIS supporters to spend a lot of bandwidth rebuilding the network instead of recruiting and promoting their views," he added.
Rashad Ali, a senior fellow at the Institute for Strategic Dialogue which works on ways to counter extremism said the approach did have merit.
"The action is both positive and negative," he said.
"Practically speaking, you are getting rid of a whole host of people from the public domain," he said, adding that such a large takedown can undoubtedly have an impact.
"However," he said, "it's not a solution because what we now need to do is not just take down accounts but actually provide new narratives for people.
"This is where we are failing," he said. "We have not had a strong, thought-out counter-argument to IS's message.