diff --git a/php/WP_CLI/Configurator.php b/php/WP_CLI/Configurator.php
index 575aebee4..fc488902f 100644
--- a/php/WP_CLI/Configurator.php
+++ b/php/WP_CLI/Configurator.php
@@ -96,6 +96,49 @@ private function load_config_spec( $path ) {
 		$this->spec = $config_spec;
 	}
 
+	/**
+	 * Add the given alias to the global config
+	 *
+	 * @param $key
+	 * @param $value
+	 * @param $yml_file_dir
+	 *
+	 * @return void
+	 */
+	private function add_alias( $key, $value, $yml_file_dir ) {
+		if ( preg_match( '#' . self::ALIAS_REGEX . '#', $key ) ) {
+			// Remove the @ character from the alias name
+			$key = substr( $key, 1 );
+		}
+
+		$this->aliases[ $key ] = [];
+		$is_alias              = false;
+		foreach ( self::$alias_spec as $i ) {
+			if ( isset( $value[ $i ] ) ) {
+				if ( 'path' === $i && ! isset( $value['ssh'] ) ) {
+					self::absolutize( $value[ $i ], $yml_file_dir );
+				}
+				$this->aliases[ $key ][ $i ] = $value[ $i ];
+				$is_alias                    = true;
+			}
+		}
+
+		// If it's not an alias, it might be a group of aliases.
+		if ( ! $is_alias && is_array( $value ) ) {
+			$alias_group = [];
+			foreach ( $value as $k ) {
+				if ( preg_match( '#' . self::ALIAS_REGEX . '#', $k ) ) {
+					// Remove the @ character from the alias name
+					$alias_group[] = substr( $k, 1 );
+				} elseif ( array_key_exists( $k, $this->aliases ) ) {
+					// Check if the alias has been properly declared before adding it to the group
+					$alias_group[] = $k;
+				}
+			}
+			$this->aliases[ $key ] = $alias_group;
+		}
+	}
+
 	/**
 	 * Get declared configuration values as an array.
 	 *
@@ -257,26 +300,10 @@ public function merge_yml( $path, $current_alias = null ) {
 		$yml_file_dir = $path ? dirname( $path ) : false;
 		foreach ( $yaml as $key => $value ) {
 			if ( preg_match( '#' . self::ALIAS_REGEX . '#', $key ) ) {
-				$this->aliases[ $key ] = [];
-				$is_alias              = false;
-				foreach ( self::$alias_spec as $i ) {
-					if ( isset( $value[ $i ] ) ) {
-						if ( 'path' === $i && ! isset( $value['ssh'] ) ) {
-							self::absolutize( $value[ $i ], $yml_file_dir );
-						}
-						$this->aliases[ $key ][ $i ] = $value[ $i ];
-						$is_alias                    = true;
-					}
-				}
-				// If it's not an alias, it might be a group of aliases.
-				if ( ! $is_alias && is_array( $value ) ) {
-					$alias_group = [];
-					foreach ( $value as $k ) {
-						if ( preg_match( '#' . self::ALIAS_REGEX . '#', $k ) ) {
-							$alias_group[] = $k;
-						}
-					}
-					$this->aliases[ $key ] = $alias_group;
+				$this->add_alias( $key, $value, $yml_file_dir );
+			} elseif ( 'aliases' === $key ) {
+				foreach ( $value as $alias => $alias_config ) {
+					$this->add_alias( $alias, $alias_config, $yml_file_dir );
 				}
 			} elseif ( ! isset( $this->spec[ $key ] ) || false === $this->spec[ $key ]['file'] ) {
 				if ( isset( $this->extra_config[ $key ] )
diff --git a/php/WP_CLI/Runner.php b/php/WP_CLI/Runner.php
index 8dc80c80f..6b573bbb4 100644
--- a/php/WP_CLI/Runner.php
+++ b/php/WP_CLI/Runner.php
@@ -507,7 +507,9 @@ private function run_ssh_command( $connection_string ) {
 		}
 
 		foreach ( $wp_args as $k => $v ) {
-			if ( preg_match( '#--ssh=#', $v ) ) {
+			if ( preg_match( '#--ssh=|--alias=#', $v ) ) {
+				unset( $wp_args[ $k ] );
+			} elseif ( preg_match( '#' . Configurator::ALIAS_REGEX . '#', $v ) ) {
 				unset( $wp_args[ $k ] );
 			}
 		}
@@ -973,9 +975,19 @@ public function init_config() {
 
 		$argv = array_slice( $GLOBALS['argv'], 1 );
 
+		// Extract config from CLI args
+		list( $args, $assoc_args, $this->runtime_config ) = $configurator->parse_args( $argv );
+		list( $this->arguments, $this->assoc_args )       = self::back_compat_conversions(
+			$...

</details>

- Fixes wp-cli/wp-cli#5677

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