The new designs and features for its apps are a direct response to widespread criticism of how the firm protects user data.
Mr Zuckerberg said the company plans to put privacy first.
He acknowledged that there was much to do to rebuild trust.
In a speech to developers, Mr Zuckerberg described the firm’s new focus on privacy as “a major shift” in how the company is run.
Some of the more visible changes to those who use the firm’s products will include:
Messages sent via Messenger will be end-to-end encrypted by default, meaning Facebook itself won’t see the contents, and the platform will be fully integrated with WhatsApp
Instagram is trialling a “private like counts” feature which would hide the “likes” a post attracts from viewers, but not the account owner
There will be more “ephemeral” ways to share content in messages – meaning there will not be a permanent record of them
A WhatsApp secure payment service trialled in India is to be rolled out to other countries later this year.
The Facebook app is being redesigned to make community groups central to the newsfeed – and the distinctive blue branding is going. The redesign is rolling out in the US and then more widely straight away.
Instagram posts will no longer have to start with a photo or a video, it will be possible to share content using just text, stickers or drawings thanks to a new “create” camera mode.
“The future is private,” Mr Zuckerberg said – adding, in a nod to the tech giant’s stream of privacy scandals: “I know we don’t have the strongest reputation on privacy right now, to put it lightly”.
He said Facebook was focused on looking at ways to encode privacy across the firm’s entire infrastructure.
“It’s not going to happen overnight and to be clear we don’t have all the answers,” he said.
He has previously said that he believes that people will want to talk privately in small groups and communities in the future.
However he will have to convince the public that Facebook is the place to do this, some commentators noted.
“The big question is how it will perform in a regulated social media world in 2019 and beyond,” said social media consultant Matt Navarra.
“My verdict: it will go the distance and bounce back, but its reputation will remain in tatters for years to come.”