diff --git a/htaccess.txt b/htaccess.txt
index f9d5b801b30..551cd5e24be 100644
--- a/htaccess.txt
+++ b/htaccess.txt
@@ -77,20 +77,34 @@ Header always set X-Content-Type-Options "nosniff"
 	# RewriteBase /
 
 	## Begin - Joomla! core SEF Section.
-	#
-	RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]
-	#
-	# If the requested path and file is not /index.php and the request
-	# has not already been internally rewritten to the index.php script
-	RewriteCond %{REQUEST_URI} !^/index\.php
-	# and the requested path and file doesn't directly match a physical file
-	RewriteCond %{REQUEST_FILENAME} !-f
-	# and the requested path and file doesn't directly match a physical folder
-	RewriteCond %{REQUEST_FILENAME} !-d
-	# internally rewrite the request to the index.php script
-	RewriteRule .* index.php [L]
-	#
-	## End - Joomla! core SEF Section.
+    #
+    # PHP FastCGI fix for HTTP Authorization, required for the API application
+    RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]
+    # -- SEF URLs for the API application
+    # If the requested path starts with /api, the file is not /api/index.php
+    # and the request has not already been internally rewritten to the
+    # api/index.php script
+    RewriteCond %{REQUEST_URI} ^/api/
+    RewriteCond %{REQUEST_URI} !^/api/index\.php
+    # and the requested path and file doesn't directly match a physical file
+    RewriteCond %{REQUEST_FILENAME} !-f
+    # and the requested path and file doesn't directly match a physical folder
+    RewriteCond %{REQUEST_FILENAME} !-d
+    # internally rewrite the request to the /api/index.php script
+    RewriteRule .* api/index.php [L]
+    # -- SEF URLs for the public frontend application
+    # If the requested path and file is not /index.php and the request
+    # has not already been internally rewritten to the index.php script
+    RewriteCond %{REQUEST_URI} !^/index\.php
+    # and the requested path and file doesn't directly match a physical file
+    RewriteCond %{REQUEST_FILENAME} !-f
+    # and the requested path and file doesn't directly match a physical folder
+    RewriteCond %{REQUEST_FILENAME} !-d
+    # internally rewrite the request to the index.php script
+    RewriteRule .* index.php [L]
+    #
+    ## End - Joomla! core SEF Section.
+
 </IfModule>
 
 ## These directives are only enabled if the Apache mod_rewrite module is disabled
diff --git a/libraries/src/Router/ApiRouter.php b/libraries/src/Router/ApiRouter.php
index 11341039064..b89e6dbdf9e 100644
--- a/libraries/src/Router/ApiRouter.php
+++ b/libraries/src/Router/ApiRouter.php
@@ -115,18 +115,8 @@ class ApiRouter extends Router
 		// Remove the base URI path.
 		$path = substr_replace($path, '', 0, \strlen($baseUri));
 
-		if (!$this->app->get('sef_rewrite'))
-		{
-			// Transform the route
-			if ($path === 'index.php')
-			{
-				$path = '';
-			}
-			else
-			{
-				$path = str_replace('index.php/', '', $path);
-			}
-		}
+		// Transform the route
+		$path = $this->removeIndexPhpFromPath($path);
 
 		$query = Uri::getInstance()->getQuery(true);
 
@@ -159,4 +149,34 @@ class ApiRouter extends Router
 
 		throw new RouteNotFoundException(sprintf('Unable to handle request for route `%s`.', $path));
 	}
+
+	/**
+	 * Removes the index.php from the route's path.
+	 *
+	 * @param   string  $path
+	 *
+	 * @return  string
+	 *
+	 * @since   4.0.0
+	 */
+	private function removeIndexPhpFromPath(string $path): string
+	{
+		// Normalize the path
+		$path = ltrim($path, '/');
+
+		// We can only remove index.php if it's present in the beginning of the route
+		if (strpos($path, 'index.php') !== 0)
+		{
+			return $path;
+		}
+
+		// Edge case: the route is index.php without a trailing slash. Bad idea but we can still map it to a null route.
+		if ($path === 'index.php')
+		{
+			return '';
+		}
+
+		// Remove the "index.php/" part of the route and return the result.
+		return substr($path, 10);
+	}
 }
diff --git a/web.config.txt b/web.config.txt
index 897d509ecdf..a3fc862dae8 100644
--- a/web.config.txt
+++ b/web.config.txt
@@ -5,7 +5,7 @@
        <directoryBrowse enabled="false" />
        <rewrite>
            <rules>
-               <rule name="Joomla! Rule 1" stopProcessing="true">
+               <rule name="Joomla! Common Exploits Prevention" stopProcessing="true">
                    <match url="^(.*)$" ignoreCase="false" />
                    <conditions logicalGrouping="MatchAny">
                        <add input="{QUERY_STRING}" pattern="base64_encode[^(]*\([^)]*\)" ignoreCase="false" />
@@ -15,7 +15,16 @@
                    </conditions>
                    <action type="CustomResponse" url="index.php" statusCode="403" statusReason="Forbidden" statusDescription="Forbidden" />
                </rule>
-               <rule name="Joomla! Rule 2">
+               <rule name="Joomla! API Application SEF URLs">
+                   <match url="^api/(.*)" ignoreCase="false" />
+                   <conditions logicalGrouping="MatchAll">
+                     <add input="{URL}" pattern="^/api/index.php" ignoreCase="true" negate="true" />
+                     <add input="{REQUEST_FILENAME}" matchType="IsFile" ignoreCase="false" negate="true" />
+                     <add input="{REQUEST_FILENAME}" matchType="IsDirectory" ignoreCase="false" negate="true" />
+                   </conditions>
+                   <action type="Rewrite" url="api/index.php" />
+               </rule>
+               <rule name="Joomla! Public Frontend SEF URLs">
                    <match url="(.*)" ignoreCase="false" />
                    <conditions logicalGrouping="MatchAll">
                      <add input="{URL}" pattern="^/index.php" ignoreCase="true" negate="true" />