How do I change a user's Email address in MediaWiki

UPDATE user SET user_email='[email protected]' WHERE user_id=... should just work. However, if you need to also set the confirmed flag, see instructions here (replace the mwscript line with php maintenance/eval.php). If you need to set their email only so that they could reset their password, see https://www.mediawiki.org/wiki/Manual:Resetting_passwords

You can get a current list of users and emails like this (i.e. decode):

SELECT Cast(user_name AS CHAR), Cast(User_Email AS CHAR) FROM user;

MaxSem's answer did not work for me, but here is a MediaWiki maintenance script (introduced in v1.27) that'll do the trick: https://www.mediawiki.org/wiki/Manual:ResetUserEmail.php

Go to the base directory of your wiki, and type something like this:
php maintenance/resetUserEmail.php uuuu [email protected]
to change user uuuu's email address to [email protected]. By default, this will change the user's password so that the user has to reset it, which can usually be done on the wiki website. You might need to add user name and password for database access, e.g.:
php maintenance/resetUserEmail.php --dbuser myuser --dbpass wordpass uuuu [email protected]