diff --git a/admin/tool/uploadcourse/classes/course.php b/admin/tool/uploadcourse/classes/course.php
index c23c25ffbae..7656ae8b593 100644
--- a/admin/tool/uploadcourse/classes/course.php
+++ b/admin/tool/uploadcourse/classes/course.php
@@ -693,7 +693,15 @@ class tool_uploadcourse_course {
             return false;
         }
 
-        // TODO MDL-59259 allow to set course format options for the current course format.
+        // Add data for course format options.
+        if (isset($coursedata['format']) || $exists) {
+            if (isset($coursedata['format'])) {
+                $courseformat = course_get_format((object)['format' => $coursedata['format']]);
+            } else {
+                $courseformat = course_get_format($existingdata);
+            }
+            $coursedata += $courseformat->validate_course_format_options($this->rawdata);
+        }
 
         // Special case, 'numsections' is not a course format option any more but still should apply from defaults.
         if (!$exists || !array_key_exists('numsections', $coursedata)) {
diff --git a/admin/tool/uploadcourse/tests/course_test.php b/admin/tool/uploadcourse/tests/course_test.php
index f52ec31d8b2..4896658807f 100644
--- a/admin/tool/uploadcourse/tests/course_test.php
+++ b/admin/tool/uploadcourse/tests/course_test.php
@@ -99,7 +99,8 @@ class tool_uploadcourse_course_testcase extends advanced_testcase {
         $this->assertTrue($co->prepare());
         $this->assertFalse($DB->record_exists('course', array('shortname' => 'newcourse')));
         $co->proceed();
-        $this->assertTrue($DB->record_exists('course', array('shortname' => 'newcourse')));
+        $course = $DB->get_record('course', array('shortname' => 'newcourse'), '*', MUST_EXIST);
+        $this->assertEquals(0, course_get_format($course)->get_course()->coursedisplay);
 
         // Try to add a new course, that already exists.
         $coursecount = $DB->count_records('course', array());
@@ -118,6 +119,16 @@ class tool_uploadcourse_course_testcase extends advanced_testcase {
         $this->assertTrue($co->prepare());
         $co->proceed();
         $this->assertTrue($DB->record_exists('course', array('shortname' => 'c2')));
+
+        // Add a new course with non-default course format option.
+        $mode = tool_uploadcourse_processor::MODE_CREATE_NEW;
+        $data = array('shortname' => 'c3', 'fullname' => 'C3', 'summary' => 'New c3', 'category' => 1,
+            'format' => 'weeks', 'coursedisplay' => 1);
+        $co = new tool_uploadcourse_course($mode, $updatemode, $data);
+        $this->assertTrue($co->prepare());
+        $co->proceed();
+        $course = $DB->get_record('course', array('shortname' => 'c3'), '*', MUST_EXIST);
+        $this->assertEquals(1, course_get_format($course)->get_course()->coursedisplay);
     }
 
     public function test_create_with_sections() {
@@ -260,6 +271,16 @@ class tool_uploadcourse_course_testcase extends advanced_testcase {
         $this->assertTrue($co->prepare());
         $co->proceed();
         $this->assertEquals('Use this summary', $DB->get_field_select('course', 'summary', 'shortname = :s', array('s' => 'c1')));
+
+        // Update course format option.
+        $mode = tool_uploadcourse_processor::MODE_UPDATE_ONLY;
+        $updatemode = tool_uploadcourse_processor::UPDATE_ALL_WITH_DATA_ONLY;
+        $data = array('shortname' => 'c1', 'coursedisplay' => 1);
+        $co = new tool_uploadcourse_course($mode, $updatemode, $data);
+        $this->assertTrue($co->prepare());
+        $co->proceed();
+        $course = $DB->get_record('course', array('shortname' => 'c1'), '*', MUST_EXIST);
+        $this->assertEquals(1, course_get_format($course)->get_course()->coursedisplay);
     }
 
     public function test_data_saved() {
diff --git a/course/format/lib.php b/course/format/lib.php
index 045d0499f94..f70371c1137 100644
--- a/course/format/lib.php
+++ b/course/format/lib.php
@@ -735,6 +735,43 @@ abstract class format_base {
         return array();
     }
 
+    /**
+     * Prepares values of course or section format options before storing them in DB
+     *
+     * If an option has invalid value it is not returned
+     *
+     * @param array $rawdata associative array of the proposed course/section format options
+     * @param int|null $sectionid null if it is course format option
+     * @return array array of options that have valid values
+     */
+    protected function validate_format_options(array $rawdata, int $sectionid = null) : array {
+        if (!$sectionid) {
+            $allformatoptions = $this->course_format_options(true);
+        } else {
+            $allformatoptions = $this->section_format_options(true);
+        }
+        $data = array_intersect_key($rawdata, $allformatoptions);
+        foreach ($data as $key => $value) {
+            $option = $allformatoptions[$key] + ['type' => PARAM_RAW, 'element_type' => null, 'element_attributes' => [[]]];
+            $data[$key] = clean_param($value, $option['type']);
+            if ($option['element_type'] === 'select' && !array_key_exists($data[$key], $option['element_attributes'][0])) {
+                // Value invalid for select element, skip.
+                unset($data[$key]);
+            }
+        }
+        return $data;
+    }
+
+    /**
+     * Validates format options for the course
+     *
+     * @param array $data data to insert/update
+     * @return array array of options that have valid values
+     */
+    public function validate_course_format_options(array $data) : array {
+        return $this->validate_format_options($data);
+    }
+
     /**
      * Updates format options for a course or section
      *
@@ -747,6 +784,7 @@ abstract class format_base {
      */
     protected function update_format_options($data, $sectionid = null) {
         global $DB;
+        $data = $this->validate_format_options((array)$data, $sectionid);
         if (!$sectionid) {
             $allformatoptions = $this->course_format_options();
             $sectionid = 0;
@@ -772,7 +810,6 @@ abstract class format_base {
                       'sectionid' => $sectionid
                     ), '', 'name,id,value');
         $changed = $needrebuild = false;
-        $data = (array)$data;
         foreach ($defaultoptions as $key => $value) {
             if (isset($records[$key])) {
                 if (array_key_exists($key, $data) && $records[$key]->value !== $data[$key]) {
diff --git a/course/format/upgrade.txt b/course/format/upgrade.txt
index 394bf21362b..16a2c668039 100644
--- a/course/format/upgrade.txt
+++ b/course/format/upgrade.txt
@@ -2,6 +2,13 @@ This files describes API changes for course formats
 
 Overview of this plugin type at http://docs.moodle.org/dev/Course_formats
 
+=== 3.6 ===
+* New method validate_format_options() cleans the values of the course/section format options before inserting them
+  in the database. Course format options can now be set in tool_uploadcourse and validation of user-submitted data is important.
+  Note that validate_format_options() is now always called when somebody creates or edits course or section and also
+  during restore and course upload. Default implementation validates against the definition of the form elements for
+  format options.
+
 === 3.5 ===
 * Course formats should overwrite get_config_for_external function to return the course format settings viewable by the
   current user.