diff --git a/admin/tool/usertours/classes/tour.php b/admin/tool/usertours/classes/tour.php
index 4c4a2014790..0765ee35155 100644
--- a/admin/tool/usertours/classes/tour.php
+++ b/admin/tool/usertours/classes/tour.php
@@ -557,9 +557,10 @@ class tour {
 
         // Remove the configuration for the tour.
         $DB->delete_records('tool_usertours_tours', array('id' => $this->id));
-
         helper::reset_tour_sortorder();
 
+        $this->remove_user_preferences();
+
         return null;
     }
 
@@ -585,6 +586,16 @@ class tour {
         return $this;
     }
 
+    /**
+     * Remove stored user preferences for the tour
+     */
+    protected function remove_user_preferences(): void {
+        global $DB;
+
+        $DB->delete_records('user_preferences', ['name' => self::TOUR_LAST_COMPLETED_BY_USER . $this->get_id()]);
+        $DB->delete_records('user_preferences', ['name' => self::TOUR_REQUESTED_BY_USER . $this->get_id()]);
+    }
+
     /**
      * Whether this tour should be displayed to the user.
      *
@@ -665,11 +676,9 @@ class tour {
      * @return  $this
      */
     public function mark_major_change() {
-        global $DB;
-
         // Clear old reset and completion notes.
-        $DB->delete_records('user_preferences', ['name' => self::TOUR_LAST_COMPLETED_BY_USER . $this->get_id()]);
-        $DB->delete_records('user_preferences', ['name' => self::TOUR_REQUESTED_BY_USER . $this->get_id()]);
+        $this->remove_user_preferences();
+
         $this->set_config('majorupdatetime', time());
         $this->persist();
 
diff --git a/admin/tool/usertours/db/upgrade.php b/admin/tool/usertours/db/upgrade.php
index 6769e01ca47..e3c0fc92441 100644
--- a/admin/tool/usertours/db/upgrade.php
+++ b/admin/tool/usertours/db/upgrade.php
@@ -25,6 +25,7 @@
 defined('MOODLE_INTERNAL') || die();
 
 use tool_usertours\manager;
+use tool_usertours\tour;
 
 /**
  * Upgrade the user tours plugin.
@@ -57,5 +58,26 @@ function xmldb_tool_usertours_upgrade($oldversion) {
     // Automatically generated Moodle v3.9.0 release upgrade line.
     // Put any upgrade step following this.
 
+    if ($oldversion < 2020082700) {
+        // Clean up user preferences of deleted tours.
+        $select = $DB->sql_like('name', ':lastcompleted') . ' OR ' . $DB->sql_like('name', ':requested');
+        $params = [
+            'lastcompleted' => tour::TOUR_LAST_COMPLETED_BY_USER . '%',
+            'requested' => tour::TOUR_REQUESTED_BY_USER . '%',
+        ];
+
+        $preferences = $DB->get_records_select('user_preferences', $select, $params, '', 'DISTINCT name');
+        foreach ($preferences as $preference) {
+            // Match tour ID at the end of the preference name, remove all of that preference type if tour ID doesn't exist.
+            if (preg_match('/(?<tourid>\d+)$/', $preference->name, $matches) &&
+                    !$DB->record_exists('tool_usertours_tours', ['id' => $matches['tourid']])) {
+
+                $DB->delete_records('user_preferences', ['name' => $preference->name]);
+            }
+        }
+
+        upgrade_plugin_savepoint(true, 2020082700, 'tool', 'usertours');
+    }
+
     return true;
 }
diff --git a/admin/tool/usertours/tests/tour_test.php b/admin/tool/usertours/tests/tour_test.php
index d08a9df79b9..c5bf23f012a 100644
--- a/admin/tool/usertours/tests/tour_test.php
+++ b/admin/tool/usertours/tests/tour_test.php
@@ -64,7 +64,7 @@ class tour_testcase extends advanced_testcase {
     /**
      * Helper to mock the database.
      *
-     * @return moodle_database
+     * @return \PHPUnit\Framework\MockObject\MockObject
      */
     public function mock_database() {
         global $DB;
@@ -569,9 +569,14 @@ class tour_testcase extends advanced_testcase {
 
         // Mock the database.
         $DB = $this->mock_database();
-        $DB->expects($this->once())
+
+        $DB->expects($this->exactly(3))
             ->method('delete_records')
-            ->with($this->equalTo('tool_usertours_tours'), $this->equalTo(['id' => $id]))
+            ->withConsecutive(
+                [$this->equalTo('tool_usertours_tours'), $this->equalTo(['id' => $id])],
+                [$this->equalTo('user_preferences'), $this->equalTo(['name' => tour::TOUR_LAST_COMPLETED_BY_USER . $id])],
+                [$this->equalTo('user_preferences'), $this->equalTo(['name' => tour::TOUR_REQUESTED_BY_USER . $id])]
+            )
             ->willReturn(null)
             ;
 
diff --git a/admin/tool/usertours/version.php b/admin/tool/usertours/version.php
index c477167923a..e34cc473e8c 100644
--- a/admin/tool/usertours/version.php
+++ b/admin/tool/usertours/version.php
@@ -24,6 +24,6 @@
 
 defined('MOODLE_INTERNAL') || die();
 
-$plugin->version   = 2020061501;            // The current module version (Date: YYYYMMDDXX).
+$plugin->version   = 2020082700;            // The current module version (Date: YYYYMMDDXX).
 $plugin->requires  = 2020060900;            // Requires this Moodle version.
 $plugin->component = 'tool_usertours';      // Full name of the plugin (used for diagnostics).