Introduction
Guide updated and tested in June 2021.
This guide has been tested from Ubuntu 20.10 to 16.04. It should also work for other Debian-based distributions without issue. For CentOS users, please refer to the comments section at the end of this page as commands will be different. I will try to update this guide for CentOS as soon as I get the chance to test it. In the meantime, if you have any suggestions on how to improve this guide, please let me know in the comments.
1. Back up phpMyAdmin
You should back up your current phpMyAdmin folder by renaming it.
sudo mv /usr/share/phpmyadmin/ /usr/share/phpmyadmin.bak
Create a new phpMyAdmin folder
sudo mkdir /usr/share/phpmyadmin/
Change to directory
cd /usr/share/phpmyadmin/
2. Download and Extract phpMyAdmin
Update Feb 2020: phpMyAdmin 5 has been released but it is only compatible with PHP 7.1 and above. To find out your PHP version in command line, run php -v.
phpMyAdmin version 4.x is now in the LTS phase, where only security fixes and critical bug fixes are made. Users are advised to migrate to version 5 (read more).
- For PHP 7.1 and above, download phpMyAdmin 5.x
- For PHP 5.5 to PHP 7.4, download phpMyAdmin-4.9.7
Visit the phpMyAdmin download page and look for the .tar.gz URL and download it using wget. In this guide we are using version 5.1.1, released June 2021. If a later version is now available, make sure to change the commands below to match (and let me know in the comments so I can update the guide 😉). If you are having issues with phpMyAdmin 5.x, try phpMyAdmin-4.9.7 instead.
sudo wget https://files.phpmyadmin.net/phpMyAdmin/5.1.1/phpMyAdmin-5.1.1-all-languages.tar.gz
Now extract
sudo tar xzf phpMyAdmin-5.1.1-all-languages.tar.gz
Once extracted, list folder
ls
You should see a new folder phpMyAdmin-5.1.1-all-languages
We want to move the contents of this folder to /usr/share/phpmyadmin
sudo mv phpMyAdmin-5.1.1-all-languages/* /usr/share/phpmyadmin
You can now log back into phpMyAdmin and check the current version. You may also see two errors:
3. Edit vendor_config.php
3.1. $cfg[‘TempDir’] (./tmp/) is not accessible
If you are seeing an error The $cfg[‘TempDir’] (./tmp/) is not accessible. phpMyAdmin is not able to cache templates and will be slow because of this.
Open vendor_config.php
sudo nano /usr/share/phpmyadmin/libraries/vendor_config.php
Press CTRL + W and search for TEMP_DIR
If you see something like below, delete it.
/usr/share/phpmyadmin/libraries/vendor_config.php
define('TEMP_DIR', ROOT_PATH . 'tmp' . DIRECTORY_SEPARATOR);
Add new line:
/usr/share/phpmyadmin/libraries/vendor_config.php
define('TEMP_DIR', '/var/lib/phpmyadmin/tmp/');
Save file and exit. (Press CTRL + X, press Y and then press ENTER)
3.2. blowfish_secret
You may also see an error The configuration file now needs a secret passphrase (blowfish_secret). The blowfish secret is used by phpMyAdmin for cookie authentication. 
Open vendor_config.php
sudo nano /usr/share/phpmyadmin/libraries/vendor_config.php
Press CTRL + W and search for CONFIG_DIR
Change line to
/usr/share/phpmyadmin/libraries/vendor_config.php
define('CONFIG_DIR', '/etc/phpmyadmin/');
phpMyAdmin will now generate its own blowfish secret based on the install directory.
Save file and exit. (Press CTRL + X, press Y and then press ENTER)
3.3. Log back in
Now log back in to phpMyAdmin and ensure the errors are gone.
If you are seeing an error “The secret passphrase in configuration (blowfish_secret) is too short.”, see below.
If you are having issues with phpMyAdmin 5, try phpMyAdmin-4.9.7 instead as this is the latest stable release for PHP 7.0 and lower and MySQL 5.4 and lower.
4. Cleanup
You can now delete the tar.gz file and the empty folder.
sudo rm /usr/share/phpmyadmin/phpMyAdmin-5.1.1-all-languages.tar.gz
sudo rm -rf /usr/share/phpmyadmin/phpMyAdmin-5.1.1-all-languages
And if you’re certain your new phpMyAdmin install is working correctly you can delete the backup folder.
sudo rm -rf /usr/share/phpmyadmin.bak
Hurrah!
Blowfish Secret Error “Too Short”
If you are seeing an error “The secret passphrase in configuration (blowfish_secret) is too short.”
Open blowfish_secret.inc.php:
sudo nano /var/lib/phpmyadmin/blowfish_secret.inc.php
Click here to generate a 32-character random phrase.
Copy it and paste it into blowfish_secret.inc.php.
/var/lib/phpmyadmin/blowfish_secret.inc.php
<?php
$cfg['blowfish_secret'] = '32_char_random_phrase_here';
Save and exit (press CTRL + X, press Y and then press ENTER)