Installation

wget https://bin.equinox.io/c/VdrWdbjqyF/cloudflared-stable-linux-amd64.deb
sudo apt-get install ./cloudflared-stable-linux-amd64.deb  
cloudflared -v

Configuration

sudo useradd -s /usr/sbin/nologin -r -M cloudflared
sudo nano /etc/default/cloudflared

# Commandline args for cloudflared
CLOUDFLARED_OPTS=--port 5053 --upstream https://1.1.1.1/dns-query --upstream https://1.0.0.1/dns-query

Update the permissions for the configuration file and cloudflared binary to allow access for the cloudflared user:
sudo chown cloudflared:cloudflared /etc/default/cloudflared
sudo chown cloudflared:cloudflared /usr/local/bin/cloudflared

Create cloudflared.service.
sudo nano /etc/systemd/system/cloudflared.service
                    [Unit]
                    Description=cloudflared DNS over HTTPS proxy
                    After=syslog.target network-online.target

                    [Service]
                    Type=simple
                    User=cloudflared
                    EnvironmentFile=/etc/default/cloudflared
                    ExecStart=/usr/local/bin/cloudflared proxy-dns $CLOUDFLARED_OPTS
                    Restart=on-failure
                    RestartSec=10
                    KillMode=process

                    [Install]
                    WantedBy=multi-user.target
Enable the systemd service to run on startup, then start the service and check its status:
sudo systemctl enable cloudflared
sudo systemctl start cloudflared
sudo systemctl status cloudflared

Now test that it is working! Run the following dig command, a response should be returned similar to the one below:
dig @127.0.0.1 -p 5053 google.com