diff --git a/includes/class-wc-install.php b/includes/class-wc-install.php
index 54246268354..4c240c66e99 100644
--- a/includes/class-wc-install.php
+++ b/includes/class-wc-install.php
@@ -839,7 +839,7 @@ CREATE TABLE {$wpdb->prefix}wc_product_meta_lookup (
   KEY `virtual` (`virtual`),
   KEY `downloadable` (`downloadable`),
   KEY `stock_status` (`stock_status`),
-  KEY `stock_status` (`stock_quantity`),
+  KEY `stock_quantity` (`stock_quantity`),
   KEY min_max_price (`min_price`, `max_price`)
   ) $collate;
 		";
diff --git a/includes/class-wc-post-data.php b/includes/class-wc-post-data.php
index d7412018c1c..ba0ad454ff8 100644
--- a/includes/class-wc-post-data.php
+++ b/includes/class-wc-post-data.php
@@ -290,6 +290,7 @@ class WC_Post_Data {
 			case 'product':
 				$data_store = WC_Data_Store::load( 'product-variable' );
 				$data_store->delete_variations( $id, true );
+				$data_store->delete_from_lookup_table( $id, 'wc_product_meta_lookup' );
 				$parent_id = wp_get_post_parent_id( $id );
 
 				if ( $parent_id ) {
@@ -297,6 +298,8 @@ class WC_Post_Data {
 				}
 				break;
 			case 'product_variation':
+				$data_store = WC_Data_Store::load( 'product' );
+				$data_store->delete_from_lookup_table( $id, 'wc_product_meta_lookup' );
 				wc_delete_product_transients( wp_get_post_parent_id( $id ) );
 				break;
 			case 'shop_order':
diff --git a/includes/data-stores/class-wc-data-store-wp.php b/includes/data-stores/class-wc-data-store-wp.php
index 11d102bafaa..d5a11c8a576 100644
--- a/includes/data-stores/class-wc-data-store-wp.php
+++ b/includes/data-stores/class-wc-data-store-wp.php
@@ -512,6 +512,29 @@ class WC_Data_Store_WP {
 		return apply_filters( 'wp_search_stopwords', $stopwords );
 	}
 
+	/**
+	 * Get data to save to a lookup table.
+	 *
+	 * @since 3.6.0
+	 * @param int    $id ID of object to update.
+	 * @param string $table Lookup table name.
+	 * @return array
+	 */
+	protected function get_data_for_lookup_table( $id, $table ) {
+		return array();
+	}
+
+	/**
+	 * Get primary key name for lookup table.
+	 *
+	 * @since 3.6.0
+	 * @param string $table Lookup table name.
+	 * @return string
+	 */
+	protected function get_primary_key_for_lookup_table( $table ) {
+		return '';
+	}
+
 	/**
 	 * Update a lookup table for an object.
 	 *
@@ -540,4 +563,32 @@ class WC_Data_Store_WP {
 			wp_cache_set( 'lookup_table', $update_data, 'object_' . $id );
 		}
 	}
+
+	/**
+	 * Delete lookup table data for an ID.
+	 *
+	 * @since 3.6.0
+	 * @param int    $id ID of object to update.
+	 * @param string $table Lookup table name.
+	 */
+	public function delete_from_lookup_table( $id, $table ) {
+		global $wpdb;
+
+		$id    = absint( $id );
+		$table = sanitize_key( $table );
+
+		if ( empty( $id ) || empty( $table ) ) {
+			return false;
+		}
+
+		$pk = $this->get_primary_key_for_lookup_table( $table );
+
+		$wpdb->delete(
+			$wpdb->$table,
+			array(
+				$pk => $id,
+			)
+		);
+		wp_cache_delete( 'lookup_table', 'object_' . $id );
+	}
 }
diff --git a/includes/data-stores/class-wc-product-data-store-cpt.php b/includes/data-stores/class-wc-product-data-store-cpt.php
index 755d71c63a0..738f57df91a 100644
--- a/includes/data-stores/class-wc-product-data-store-cpt.php
+++ b/includes/data-stores/class-wc-product-data-store-cpt.php
@@ -624,7 +624,7 @@ class WC_Product_Data_Store_CPT extends WC_Data_Store_WP implements WC_Object_Da
 			}
 		}
 
-		if ( array_intersect( $this->updated_props, array( 'sku', 'regular_price', 'sale_price', 'date_on_sale_from', 'date_on_sale_to', 'total_sales', 'average_rating', 'stock_quantity', 'manage_stock' ) ) ) {
+		if ( array_intersect( $this->updated_props, array( 'sku', 'regular_price', 'sale_price', 'date_on_sale_from', 'date_on_sale_to', 'total_sales', 'average_rating', 'stock_quantity', 'stock_status', 'manage_stock', 'downloadable', 'virtual' ) ) ) {
 			$this->update_lookup_table( $product->get_id(), 'wc_product_meta_lookup' );
 		}
 
@@ -1894,4 +1894,18 @@ class WC_Product_Data_Store_CPT extends WC_Data_Store_WP implements WC_Object_Da
 		}
 		return array();
 	}
+
+	/**
+	 * Get primary key name for lookup table.
+	 *
+	 * @since 3.6.0
+	 * @param string $table Lookup table name.
+	 * @return string
+	 */
+	protected function get_primary_key_for_lookup_table( $table ) {
+		if ( 'wc_product_meta_lookup' === $table ) {
+			return 'product_id';
+		}
+		return '';
+	}
 }