# The ServerName directive sets the request scheme, hostname and port that
        # the server uses to identify itself. This is used when creating
        # redirection URLs. In the context of virtual hosts, the ServerName
        # specifies what hostname must appear in the request's Host: header to
        # match this virtual host. For the default virtual host (this file) this
        # value is not decisive as it is used as a last resort host regardless.
        # However, you must set it for any further virtual host explicitly.
        #ServerName www.example.com

<VirtualHost *:80>
        ServerAdmin koopmanng@gmail.com
        ServerName xx1.com
        ServerAlias www.xx1.com

        DocumentRoot /var/www
        <Directory />
                Options FollowSymLinks
                AllowOverride All
        </Directory>
        <Directory /var/www>
                Options Indexes FollowSymLinks MultiViews
                AllowOverride None
                Order allow,deny
                allow from all
        </Directory>
        # Available loglevels: trace8, ..., trace1, debug, info, notice, warn,
        # error, crit, alert, emerg.
        # It is also possible to configure the loglevel for particular
        # modules, e.g.
        #LogLevel info ssl:warn

        ErrorLog ${APACHE_LOG_DIR}/error.log
        CustomLog ${APACHE_LOG_DIR}/access.log combined

        # For most configuration files from conf-available/, which are
        # enabled or disabled at a global level, it is possible to
        # include a line for only one particular virtual host. For example the
        # following line enables the CGI configuration for this host only
        # after it has been globally disabled with "a2disconf".
        #Include conf-available/serve-cgi-bin.conf
</VirtualHost>

# vim: syntax=apache ts=4 sw=4 sts=4 sr noet

ServerRoot "/etc/apache2"
Mutex file:${APACHE_LOCK_DIR} default
PidFile ${APACHE_PID_FILE}
Timeout 300
KeepAlive On
MaxKeepAliveRequests 100
KeepAliveTimeout 5
User ${APACHE_RUN_USER}
Group ${APACHE_RUN_GROUP}
HostnameLookups Off
ErrorLog ${APACHE_LOG_DIR}/error.log
LogLevel crit
IncludeOptional mods-enabled/*.load
IncludeOptional mods-enabled/*.conf
Include ports.conf

<Directory />
    Options FollowSymLinks
    AllowOverride All
    <Limit PUT DELETE CONNECT OPTIONS PATCH PROPFIND PROPPATCH MKCOL COPY MOVE LOCK U$
        deny from all
    </Limit>
</Directory>

<Directory /var/www>
        Options FollowSymLinks
        AllowOverride FileInfo
</Directory>

<Directory /usr/share>
        AllowOverride All
        Require all granted
</Directory>

AccessFileName .htaccess

<FilesMatch "^\.ht">
        Require all denied
</FilesMatch>


AccessFileName .htaccess

<FilesMatch "^\.ht">
      Require all denied
</FilesMatch>

LogFormat "%v:%p %h %l %u %t \"%r\" %>s %O \"%{Referer}i\" \"%{User-Agent}i\"" vhost_$
LogFormat "%h %l %u %t \"%r\" %>s %O \"%{Referer}i\" \"%{User-Agent}i\"" combined
LogFormat "%h %l %u %t \"%r\" %>s %O" common
LogFormat "%{Referer}i -> %U" referer
LogFormat "%{User-agent}i" agent

IncludeOptional conf-enabled/*.conf
IncludeOptional sites-enabled/*.conf

#<DirectoryMatch ^.*/wp-content/uploads/>
#  AllowOverride All
#  php_flag engine off
#  php_admin_value engine Off
#</DirectoryMatch>

#<DirectoryMatch ^.*/wp-content/blogs.dir/>
#  AllowOverride All
#  php_flag engine off
#  php_admin_value engine Off
#</DirectoryMatch>

#<DirectoryMatch ^.*/wp-admin/>
#  AuthType Basic
#  AuthName "Welcome Gijs!"
#  AuthUserFile /etc/apache2/.htpasswd
#  Require valid-user
#</DirectoryMatch>

<VirtualHost *:80>
   ServerAdmin info@
   DocumentRoot /var/www
   Servername 104.236.227.62
   ServerAlias website1.com www.website1.com
 </VirtualHost>

<VirtualHost *:80>
   ServerAdmin koo
   DocumentRoot /var/www
   Servername 104.236.227.62
   ServerAlias www.xx1.com xx1.com
</VirtualHost>

<VirtualHost *:80>
   ServerAdmin info@
   DocumentRoot /var/www
   Servername 104.236.227.62
   ServerAlias www.xx2.net xx2.net
 </VirtualHost>

RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]

# add a trailing slash to /wp-admin
RewriteRule ^wp-admin$ wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule ^(wp-(content|admin|includes).*) $1 [L]
RewriteRule ^(.*\.php)$ $1 [L]
RewriteRule . index.php [L]

<?php
/**
 * The base configurations of the WordPress.
 *
 * This file has the following configurations: MySQL settings, Table Prefix,
 * Secret Keys, and ABSPATH. You can find more information by visiting
 * {@link http://codex.wordpress.org/Editing_wp-config.php Editing wp-config.php}
 * Codex page. You can get the MySQL settings from your web host.
 *
 * This file is used by the wp-config.php creation script during the
 * installation. You don't have to use the web site, you can just copy this file
 * to "wp-config.php" and fill in the values.
 *
 * @package WordPress
 */

// ** MySQL settings - You can get this info from your web host ** //
/** The name of the database for WordPress */

/** MySQL database username */

/** MySQL database password */

/** MySQL hostname */
define('DB_HOST', 'localhost');

/** Database Charset to use in creating database tables. */
define('DB_CHARSET', 'utf8');

/** The Database Collate type. Don't change this if in doubt. */
define('DB_COLLATE', '');

/**#@+
 * Authentication Unique Keys and Salts.
 *
 * Change these to different unique phrases!
 * You can generate these using the {@link https://api.wordpress.org/secret-key/1.1/s$
 * You can change these at any point in time to invalidate all existing cookies. This$
 *
 * @since 2.6.0
 */

/**#@-*/

/**
 * WordPress Database Table prefix.
 *
 * You can have multiple installations in one database if you give each a unique
 * prefix. Only numbers, letters, and underscores please!
 */
$table_prefix  = 'wp_';

/**
 * For developers: WordPress debugging mode.
 *
 * Change this to true to enable the display of notices during development.
 * It is strongly recommended that plugin and theme developers use WP_DEBUG
 * in their development environments.
 */
define('WP_DEBUG', false);


define( 'WP_ALLOW_MULTISITE', true );

define('MULTISITE', true);
define('SUBDOMAIN_INSTALL', true);
define('DOMAIN_CURRENT_SITE', 'rinconolon.ec');
define('PATH_CURRENT_SITE', '/');
define('SITE_ID_CURRENT_SITE', 1);
define('BLOG_ID_CURRENT_SITE', 1);

/* That's all, stop editing! Happy blogging. */

/** Absolute path to the WordPress directory. */
if ( !defined('ABSPATH') )
        define('ABSPATH', dirname(__FILE__) . '/');

/** Sets up WordPress vars and included files. */
define('FS_METHOD', 'direct');
define('AUTH_KEY',         'Gt-$ZV!GbP{Xo+]MU<heSz Vt}K>T.fp=$=T1Qz8;Xp;$f6.d(]yj&eo,$
define('SECURE_AUTH_KEY',  'T%pl`8*;)!|Rv|+M:E4,&%m?*]|MWr&$e`]P-]p|mr|tU_MpM?#4&tKkw$
define('LOGGED_IN_KEY',    'N](HwTmt+;ub]<E+vl|I#o;dHjAN4<z]}kkN/B0+ck#PPh!QF%j/!]T=_$
define('NONCE_KEY',        '?l5$9=32Gc%xjfv)J|hUCcJpdO~A*-j`_D+.xFk;GsazRzK2G|OkFUcJY$
define('AUTH_SALT',        'Q?D*wl_UX+UgAe|0{OBT+U<qeeB&h,G7;A%V?=!N|W)@_9K0Rf2&t]0Q~$
define('SECURE_AUTH_SALT', 'h:^U=>!m0>r8K1R*3Uj-$|^EDU -o?[#>i$6ce<ph{}0jXQCC|jiPo{!X$
define('LOGGED_IN_SALT',   'u(:>jw|[._.}A;+CDa%e+JeHv&#&g8frq2+{~!QI%zvw[_ODbnlLB0C-@$
define('NONCE_SALT',       'sbx~#`(kwyMwt@R?|,&qJo|cP$!2{w,<0|z7WVMG<!E[!Bu1R_UG4,yxB$define('DB_NAME', 'wordpress');
define('DB_USER', 'wordpress');
define('DB_PASSWORD', '2Ih3ZtiRhK');
define( 'SUNRISE', 'on' );
require_once(ABSPATH . 'wp-settings.php');

http://imgur.com/MENguiH

It seems my perma-links are not working… So something went wrong somewhere…

All info (htaccess, wp-config, 000-site.conf, apache2.conf) are pasted below.

Many thanks to anyone that’s able to point me in the right direction!!!

Set the AllowOverride directive inside every <Directory /var/www> block to All.

<Directory /var/www>
[...]
AllowOverride All
[...]
</Directory>

The vhost file meant for this Multisite setup should have all the domains in `ServerAlias.

ServerName website1.com
ServerAlias *.website1.com xx1.com xx2.net

Ensure mod_rewrite is enabled:

sudo apachectl -M | grep rewrite

If not enable it:

sudo a2enmod rewrite
sudo service apache2 reload