The Tor Project maintains an official Debian package repository deb.torproject.org, which is also served through via an Onion Service: http://apow7mjfryruh65chtdydfmqfpj5btws7nbocgtaovhvezgccyjazpqd.onion/

To use Apt over Tor, the apt transport needs to be installed:

   $ sudo apt install apt-transport-tor

Then you need to add the following entries to /etc/apt/sources.list or a new file in /etc/apt/sources.list.d/:

   # For the stable version.
   deb [signed-by=/usr/share/keyrings/deb.torproject.org-keyring.gpg] tor+http://apow7mjfryruh65chtdydfmqfpj5btws7nbocgtaovhvezgccyjazpqd.onion/torproject.org <DISTRIBUTION> main

   # For the unstable version.
   deb [signed-by=/usr/share/keyrings/deb.torproject.org-keyring.gpg] tor+http://apow7mjfryruh65chtdydfmqfpj5btws7nbocgtaovhvezgccyjazpqd.onion/torproject.org tor-nightly-main-<DISTRIBUTION> main

Replace <DISTRIBUTION> with your Operating System codename. Run lsb_release -c or cat /etc/debian_version to check the Operating System version.

Since Debian bookworm you can also use the more modern deb822-style:

   # echo "\
     Types: deb deb-src
     Components: main
     Suites: bookworm
     URIs: tor+http://apow7mjfryruh65chtdydfmqfpj5btws7nbocgtaovhvezgccyjazpqd.onion/torproject.org
     Architectures: amd64 arm64 i386
     Signed-By: /usr/share/keyrings/deb.torproject.org-keyring.gpg
     " | sudo tee /etc/apt/sources.list.d/tor.sources

For onion services run by the Debian project, please refer to their official documentation.