diff --git a/backup/moodle2/backup_stepslib.php b/backup/moodle2/backup_stepslib.php
index 5549fdb88a4..8f82b94d3fc 100644
--- a/backup/moodle2/backup_stepslib.php
+++ b/backup/moodle2/backup_stepslib.php
@@ -546,9 +546,11 @@ class backup_course_structure_step extends backup_structure_step {
                                      backup_helper::is_sqlparam('course'),
                                      backup::VAR_PARENTID));
 
+        // Section level settings are dealt with in backup_section_structure_step.
+        // We only need to deal with course level (sectionid = 0) here.
         $courseformatoption->set_source_sql('SELECT id, format, sectionid, name, value
                                  FROM {course_format_options}
-                                 WHERE courseid = ?', [ backup::VAR_PARENTID ]);
+                                 WHERE courseid = ? AND sectionid = 0', [ backup::VAR_PARENTID ]);
 
         $handler = core_course\customfield\course_handler::create();
         $fieldsforbackup = $handler->get_instance_data_for_backup($this->task->get_courseid());
diff --git a/backup/moodle2/restore_stepslib.php b/backup/moodle2/restore_stepslib.php
index e61c2d139d8..b1b9768079a 100644
--- a/backup/moodle2/restore_stepslib.php
+++ b/backup/moodle2/restore_stepslib.php
@@ -1952,6 +1952,10 @@ class restore_course_structure_step extends restore_structure_step {
         // Course record ready, update it
         $DB->update_record('course', $data);
 
+        // Apply any course format options that may be saved against the course
+        // entity in earlier-version backups.
+        course_get_format($data)->update_course_format_options($data);
+
         // Role name aliases
         restore_dbops::set_course_role_names($this->get_restoreid(), $this->get_courseid());
     }
@@ -1989,8 +1993,14 @@ class restore_course_structure_step extends restore_structure_step {
     public function process_course_format_option(array $data) : void {
         global $DB;
 
+        if ($data['sectionid']) {
+            // Ignore section-level format options saved course-level in earlier-version backups.
+            return;
+        }
+
         $courseid = $this->get_courseid();
-        $record = $DB->get_record('course_format_options', [ 'courseid' => $courseid, 'name' => $data['name'] ], 'id');
+        $record = $DB->get_record('course_format_options', [ 'courseid' => $courseid, 'name' => $data['name'],
+                'format' => $data['format'], 'sectionid' => 0 ], 'id');
         if ($record !== false) {
             $DB->update_record('course_format_options', (object) [ 'id' => $record->id, 'value' => $data['value'] ]);
         } else {