diff --git a/src/wp-includes/class-wp-theme-json.php b/src/wp-includes/class-wp-theme-json.php
index 486156fcd3..b140601a43 100644
--- a/src/wp-includes/class-wp-theme-json.php
+++ b/src/wp-includes/class-wp-theme-json.php
@@ -1106,8 +1106,8 @@ class WP_Theme_JSON {
 		foreach ( $nodes as $metadata ) {
 			foreach ( $to_replace as $property_path ) {
 				$path = array_merge( $metadata['path'], $property_path );
-				$node = _wp_array_get( $incoming_data, $path, array() );
-				if ( ! empty( $node ) ) {
+				$node = _wp_array_get( $incoming_data, $path, null );
+				if ( isset( $node ) ) {
 					_wp_array_set( $this->theme_json, $path, $node );
 				}
 			}
diff --git a/tests/phpunit/tests/theme/wpThemeJson.php b/tests/phpunit/tests/theme/wpThemeJson.php
index 0b4f8268bf..27294aac96 100644
--- a/tests/phpunit/tests/theme/wpThemeJson.php
+++ b/tests/phpunit/tests/theme/wpThemeJson.php
@@ -667,6 +667,209 @@ class Tests_Theme_wpThemeJson extends WP_UnitTestCase {
 		$this->assertEqualSetsWithIndex( $expected, $actual );
 	}
 
+	/**
+	 * @ticket 53175
+	 */
+	public function test_merge_incoming_data_empty_presets() {
+		$theme_json = new WP_Theme_JSON(
+			array(
+				'version'  => WP_Theme_JSON::LATEST_SCHEMA,
+				'settings' => array(
+					'color'      => array(
+						'duotone'   => array(
+							array(
+								'slug'   => 'value',
+								'colors' => array( 'red', 'green' ),
+							),
+						),
+						'gradients' => array(
+							array(
+								'slug'     => 'gradient',
+								'gradient' => 'gradient',
+							),
+						),
+						'palette'   => array(
+							array(
+								'slug'  => 'red',
+								'color' => 'red',
+							),
+						),
+					),
+					'spacing'    => array(
+						'units' => array( 'px', 'em' ),
+					),
+					'typography' => array(
+						'fontSizes' => array(
+							array(
+								'slug'  => 'size',
+								'value' => 'size',
+							),
+						),
+					),
+				),
+			)
+		);
+
+		$theme_json->merge(
+			new WP_Theme_JSON(
+				array(
+					'version'  => WP_Theme_JSON::LATEST_SCHEMA,
+					'settings' => array(
+						'color'      => array(
+							'duotone'   => array(),
+							'gradients' => array(),
+							'palette'   => array(),
+						),
+						'spacing'    => array(
+							'units' => array(),
+						),
+						'typography' => array(
+							'fontSizes' => array(),
+						),
+					),
+				)
+			)
+		);
+
+		$actual   = $theme_json->get_raw_data();
+		$expected = array(
+			'version'  => WP_Theme_JSON::LATEST_SCHEMA,
+			'settings' => array(
+				'color'      => array(
+					'duotone'   => array(),
+					'gradients' => array(
+						'theme' => array(),
+					),
+					'palette'   => array(
+						'theme' => array(),
+					),
+				),
+				'spacing'    => array(
+					'units' => array(),
+				),
+				'typography' => array(
+					'fontSizes' => array(
+						'theme' => array(),
+					),
+				),
+			),
+		);
+
+		$this->assertEqualSetsWithIndex( $expected, $actual );
+	}
+
+	/**
+	 * @ticket 53175
+	 */
+	public function test_merge_incoming_data_null_presets() {
+		$theme_json = new WP_Theme_JSON(
+			array(
+				'version'  => WP_Theme_JSON::LATEST_SCHEMA,
+				'settings' => array(
+					'color'      => array(
+						'duotone'   => array(
+							array(
+								'slug'   => 'value',
+								'colors' => array( 'red', 'green' ),
+							),
+						),
+						'gradients' => array(
+							array(
+								'slug'     => 'gradient',
+								'gradient' => 'gradient',
+							),
+						),
+						'palette'   => array(
+							array(
+								'slug'  => 'red',
+								'color' => 'red',
+							),
+						),
+					),
+					'spacing'    => array(
+						'units' => array( 'px', 'em' ),
+					),
+					'typography' => array(
+						'fontSizes' => array(
+							array(
+								'slug'  => 'size',
+								'value' => 'size',
+							),
+						),
+					),
+				),
+			)
+		);
+
+		$theme_json->merge(
+			new WP_Theme_JSON(
+				array(
+					'version'  => WP_Theme_JSON::LATEST_SCHEMA,
+					'settings' => array(
+						'color'      => array(
+							'custom' => false,
+						),
+						'spacing'    => array(
+							'customMargin' => false,
+						),
+						'typography' => array(
+							'customLineHeight' => false,
+						),
+					),
+				)
+			)
+		);
+
+		$actual   = $theme_json->get_raw_data();
+		$expected = array(
+			'version'  => WP_Theme_JSON::LATEST_SCHEMA,
+			'settings' => array(
+				'color'      => array(
+					'custom'    => false,
+					'duotone'   => array(
+						array(
+							'slug'   => 'value',
+							'colors' => array( 'red', 'green' ),
+						),
+					),
+					'gradients' => array(
+						'theme' => array(
+							array(
+								'slug'     => 'gradient',
+								'gradient' => 'gradient',
+							),
+						),
+					),
+					'palette'   => array(
+						'theme' => array(
+							array(
+								'slug'  => 'red',
+								'color' => 'red',
+							),
+						),
+					),
+				),
+				'spacing'    => array(
+					'customMargin' => false,
+					'units'        => array( 'px', 'em' ),
+				),
+				'typography' => array(
+					'customLineHeight' => false,
+					'fontSizes'        => array(
+						'theme' => array(
+							array(
+								'slug'  => 'size',
+								'value' => 'size',
+							),
+						),
+					),
+				),
+			),
+		);
+
+		$this->assertEqualSetsWithIndex( $expected, $actual );
+	}
+
 	/**
 	 * @ticket 52991
 	 */