diff --git b/src/wp-includes/taxonomy.php a/src/wp-includes/taxonomy.php
index c60f1df..c898cbf 100644
--- b/src/wp-includes/taxonomy.php
+++ a/src/wp-includes/taxonomy.php
@@ -3386,6 +3386,12 @@ function wp_update_term( $term_id, $taxonomy, $args = array() ) {
 
 	$tt_id = $wpdb->get_var( $wpdb->prepare( "SELECT tt.term_taxonomy_id FROM $wpdb->term_taxonomy AS tt INNER JOIN $wpdb->terms AS t ON tt.term_id = t.term_id WHERE tt.taxonomy = %s AND t.term_id = %d", $taxonomy, $term_id) );
 
+	// Check whether this is a shared term that needs splitting.
+	$_term_id = _split_shared_term( $term_id, $tt_id );
+	if ( ! is_wp_error( $_term_id ) ) {
+		$term_id = $_term_id;
+	}
+
 	/**
 	 * Fires immediately before the given terms are edited.
 	 *
@@ -4040,6 +4046,62 @@ function _update_generic_term_count( $terms, $taxonomy ) {
 }
 
 /**
+ * Create a new term for a term_taxonomy item that currently shares its term.
+ *
+ * @since 4.1.0
+ * @access private
+ *
+ * @param int   $term_id          ID of the shared term.
+ * @param int   $term_taxonomy_id ID of the term taxonomy item to receive a new term.
+ * @param array $shared_tts       Sibling term taxonomies, used for busting caches.
+ * @return int  Term ID.
+ */
+function _split_shared_term( $term_id, $term_taxonomy_id ) {
+	global $wpdb;
+
+	// Don't try to split terms if database schema does not support shared slugs.
+	$current_db_version = get_option( 'db_version' );
+	if ( $current_db_version < 30133 ) {
+		return $term_id;
+	}
+
+	// If there are no shared term_taxonomy rows, there's nothing to do here.
+	$shared_tt_count = $wpdb->get_var( $wpdb->prepare( "SELECT COUNT(*) FROM $wpdb->term_taxonomy tt WHERE tt.term_id = %d AND tt.term_taxonomy_id != %d", $term_id, $term_taxonomy_id ) );
+	if ( ! $shared_tt_count ) {
+		return $term_id;
+	}
+
+	// Pull up data about the currently shared slug, which we'll use to populate the new one.
+	$shared_term = $wpdb->get_row( $wpdb->prepare( "SELECT t.* FROM $wpdb->terms t WHERE t.term_id = %d", $term_id ) );
+
+	$new_term_data = array(
+		'name' => $shared_term->name,
+		'slug' => $shared_term->slug,
+		'term_group' => $shared_term->term_group,
+	);
+
+	if ( false === $wpdb->insert( $wpdb->terms, $new_term_data ) ) {
+		return new WP_Error( 'db_insert_error', __( 'Could not split shared term.' ), $wpdb->last_error );
+	}
+
+	$new_term_id = (int) $wpdb->insert_id;
+
+	// Update the existing term_taxonomy to point to the newly created term.
+	$wpdb->update( $wpdb->term_taxonomy,
+		array( 'term_id' => $new_term_id ),
+		array( 'term_taxonomy_id' => $term_taxonomy_id )
+	);
+
+	// Clean the cache for term taxonomies formerly shared with the current term.
+	$shared_term_taxonomies = $wpdb->get_row( $wpdb->prepare( "SELECT taxonomy FROM $wpdb->term_taxonomy WHERE term_id = %d", $term_id ) );
+	foreach ( (array) $shared_term_taxonomies as $shared_term_taxonomy ) {
+		clean_term_cache( $term_id, $shared_term_taxonomy );
+	}
+
+	return $new_term_id;
+}
+
+/**
  * Generate a permalink for a taxonomy term archive.
  *
  * @since 2.5.0
diff --git b/tests/phpunit/tests/term.php a/tests/phpunit/tests/term.php
index 2cf5fb2..1258c4b 100644
--- b/tests/phpunit/tests/term.php
+++ a/tests/phpunit/tests/term.php
@@ -690,6 +690,88 @@ class Tests_Term extends WP_UnitTestCase {
 		$this->assertSame( 'duplicate_term_slug', $updated->get_error_code() );
 	}
 
+	/**
+	 * @ticket 5809
+	 */
+	public function test_wp_update_term_should_split_shared_term() {
+		global $wpdb;
+
+		register_taxonomy( 'wptests_tax', 'post' );
+		register_taxonomy( 'wptests_tax_2', 'post' );
+
+		$t1 = wp_insert_term( 'Foo', 'wptests_tax' );
+		$t2 = wp_insert_term( 'Foo', 'wptests_tax_2' );
+
+		// Manually modify because split terms shouldn't naturally occur.
+		$wpdb->update( $wpdb->term_taxonomy,
+			array( 'term_id' => $t1['term_id'] ),
+			array( 'term_taxonomy_id' => $t2['term_taxonomy_id'] ),
+			array( '%d' ),
+			array( '%d' )
+		);
+
+		$posts = $this->factory->post->create_many( 2 );
+		wp_set_object_terms( $posts[0], array( 'Foo' ), 'wptests_tax' );
+		wp_set_object_terms( $posts[1], array( 'Foo' ), 'wptests_tax_2' );
+
+		// Verify that the terms are shared.
+		$t1_terms = wp_get_object_terms( $posts[0], 'wptests_tax' );
+		$t2_terms = wp_get_object_terms( $posts[1], 'wptests_tax_2' );
+		$this->assertSame( $t1_terms[0]->term_id, $t2_terms[0]->term_id );
+
+		wp_update_term( $t2_terms[0]->term_id, 'wptests_tax_2', array(
+			'name' => 'New Foo',
+		) );
+
+		$t1_terms = wp_get_object_terms( $posts[0], 'wptests_tax' );
+		$t2_terms = wp_get_object_terms( $posts[1], 'wptests_tax_2' );
+		$this->assertNotEquals( $t1_terms[0]->term_id, $t2_terms[0]->term_id );
+	}
+
+	/**
+	 * @ticket 5809
+	 */
+	public function test_wp_update_term_should_not_split_shared_term_before_410_schema_change() {
+		global $wpdb;
+
+		$db_version = get_option( 'db_version' );
+		update_option( 'db_version', 30055 );
+
+		register_taxonomy( 'wptests_tax', 'post' );
+		register_taxonomy( 'wptests_tax_2', 'post' );
+
+		$t1 = wp_insert_term( 'Foo', 'wptests_tax' );
+		$t2 = wp_insert_term( 'Foo', 'wptests_tax_2' );
+
+		// Manually modify because split terms shouldn't naturally occur.
+		$wpdb->update( $wpdb->term_taxonomy,
+			array( 'term_id' => $t1['term_id'] ),
+			array( 'term_taxonomy_id' => $t2['term_taxonomy_id'] ),
+			array( '%d' ),
+			array( '%d' )
+		);
+
+		$posts = $this->factory->post->create_many( 2 );
+		wp_set_object_terms( $posts[0], array( 'Foo' ), 'wptests_tax' );
+		wp_set_object_terms( $posts[1], array( 'Foo' ), 'wptests_tax_2' );
+
+		// Verify that the term is shared.
+		$t1_terms = wp_get_object_terms( $posts[0], 'wptests_tax' );
+		$t2_terms = wp_get_object_terms( $posts[1], 'wptests_tax_2' );
+		$this->assertSame( $t1_terms[0]->term_id, $t2_terms[0]->term_id );
+
+		wp_update_term( $t2_terms[0]->term_id, 'wptests_tax_2', array(
+			'name' => 'New Foo',
+		) );
+
+		// Term should still be shared.
+		$t1_terms = wp_get_object_terms( $posts[0], 'wptests_tax' );
+		$t2_terms = wp_get_object_terms( $posts[1], 'wptests_tax_2' );
+		$this->assertSame( $t1_terms[0]->term_id, $t2_terms[0]->term_id );
+
+		update_option( 'db_version', $db_version );
+	}
+
 	public function test_wp_update_term_alias_of_no_term_group() {
 		register_taxonomy( 'wptests_tax', 'post' );
 		$t1 = $this->factory->term->create( array(