diff --git a/mysql-test/r/mysqld_option_err.result b/mysql-test/r/mysqld_option_err.result
index 4afcc5e0cb1..1870ea85270 100644
--- a/mysql-test/r/mysqld_option_err.result
+++ b/mysql-test/r/mysqld_option_err.result
@@ -5,4 +5,5 @@ Test non-numeric value passed to number option.
 Test that bad value for plugin enum option is rejected correctly.
 Test that --help --verbose works
 Test that --not-known-option --help --verbose gives error
+Test that specifying same directory several times handled properly.
 Done.
diff --git a/mysql-test/t/mysqld_option_err.test b/mysql-test/t/mysqld_option_err.test
index 0c38eba7ca9..6f1e089fbe4 100644
--- a/mysql-test/t/mysqld_option_err.test
+++ b/mysql-test/t/mysqld_option_err.test
@@ -56,4 +56,12 @@ mkdir $MYSQLTEST_VARDIR/tmp/mysqld_option_err;
 --error 2
 --exec $MYSQLD_BOOTSTRAP_CMD --not-known-option --help --verbose >>$MYSQLTEST_VARDIR/tmp/mysqld_option_err/mysqltest.log 2>&1
 
+#
+# MDEV-9969 mysql_install_db error processing ignore_db_dirs.
+#
+
+--echo Test that specifying same directory several times handled properly.
+
+--exec echo "" | $MYSQLD_BOOTSTRAP_CMD --skip-networking --datadir=$MYSQLTEST_VARDIR/tmp/mysqld_option_err --skip-grant-tables --ignore-db-dirs='some_dir' --ignore-db-dirs='some_dir'  >>$MYSQLTEST_VARDIR/tmp/mysqld_option_err/mysqltest.log 2>&1
+
 --echo Done.
diff --git a/sql/sql_show.cc b/sql/sql_show.cc
index b8926b986b0..931011dcbc2 100644
--- a/sql/sql_show.cc
+++ b/sql/sql_show.cc
@@ -720,12 +720,24 @@ ignore_db_dirs_process_additions()
   for (i= 0; i < ignore_db_dirs_array.elements; i++)
   {
     get_dynamic(&ignore_db_dirs_array, (uchar *) &dir, i);
-    if (my_hash_insert(&ignore_db_dirs_hash, (uchar *) dir))
-      return true;
-    ptr= strnmov(ptr, dir->str, dir->length);
-    if (i + 1 < ignore_db_dirs_array.elements)
-      ptr= strmov(ptr, ",");
+    if (my_hash_insert(&ignore_db_dirs_hash, (uchar *)dir))
+    {
+      /* ignore duplicates from the config file */
+      if (my_hash_search(&ignore_db_dirs_hash, (uchar *)dir->str, dir->length))
+      {
+        sql_print_warning("Duplicate ignore-db-dir directory name '%.*s' "
+                          "found in the config file(s). Ignoring the duplicate.",
+                          (int) dir->length, dir->str);
+        my_free(dir);
+        goto continue_loop;
+      }
 
+      return true;
+    }
+    ptr= strnmov(ptr, dir->str, dir->length);
+    *(ptr++)= ',';
+
+continue_loop:
     /*
       Set the transferred array element to NULL to avoid double free
       in case of error.
@@ -734,6 +746,12 @@ ignore_db_dirs_process_additions()
     set_dynamic(&ignore_db_dirs_array, (uchar *) &dir, i);
   }
 
+  if (ptr > opt_ignore_db_dirs)
+  {
+    ptr--;
+    DBUG_ASSERT(*ptr == ',');
+  }
+
   /* make sure the string is terminated */
   DBUG_ASSERT(ptr - opt_ignore_db_dirs <= (ptrdiff_t) len);
   *ptr= 0;