The photo-blogging giant announced in March that it would change the feed from chronological order to the posts users are "most likely to be interested in".
In a statement on its blog, Instagram reassured users that "all the posts will still be there, just in a different order".
But some of the site's members have expressed frustration at the change, and said they want to keep the order as it is.
Tara Rees tweeted: "Haven't heard anyone say they want their Instagram feed changed, yet it's happening. Shame on you @instagram!"
Amy wrote: "I will stop using @instagram the second my home feed goes out of order."
Michael Marten said he would pay to keep his feed as it is.
He tweeted: "Hey, @instagram, I'd pay a (reasonable) annual fee if that gave the option to keep a chronological feed."
The site said the changes will mean users are less likely to miss things they most want to see - stating that currently users miss on average 70 per cent of their feeds.
Announcing the change earlier this year, Instagram said: "The order of photos and videos in your feed will be based on the likelihood you'll be interested in the content, your relationship with the person posting and the timeliness of the post."
It pledged to take the thoughts of users into account.
The post added: "We're going to take time to get this right and listen to your feedback along the way. You'll see this new experience in the coming months.