On Linux, mitmproxy integrates with the iptables redirection mechanism to achieve transparent mode.

1. Install the mitmproxy certificates on the test device.
2. Enable IP forwarding:

       sysctl -w net.ipv4.ip_forward=1

   You may also want to consider enabling this permanently in /etc/sysctl.conf.
3. If your target machine is on the same physical network and you configured it to use a custom gateway, disable ICMP redirects:

       echo 0 | sudo tee /proc/sys/net/ipv4/conf/*/send_redirects

   You may also want to consider enabling this permanently in /etc/sysctl.conf as demonstrated here.
4. Create an iptables ruleset that redirects the desired traffic to the mitmproxy port. Details will differ according to your setup, but the ruleset should look something like this:

       iptables -t nat -A PREROUTING -i eth0 -p tcp --dport 80 -j REDIRECT --to-port 8080
       iptables -t nat -A PREROUTING -i eth0 -p tcp --dport 443 -j REDIRECT --to-port 8080

5. Fire up mitmproxy. You probably want a command like this:

       mitmproxy -T --host

   The -T flag turns on transparent mode, and the --host argument tells mitmproxy to use the value of the Host header for URL display.
6. Finally, configure your test device to use the host on which mitmproxy is running as the default gateway.

For a detailed walkthrough, have a look at the Transparently proxify virtual machines tutorial.