diff --git a/sqlglot/optimizer/qualify_tables.py b/sqlglot/optimizer/qualify_tables.py
index c223f55eec..3e9935149a 100644
--- a/sqlglot/optimizer/qualify_tables.py
+++ b/sqlglot/optimizer/qualify_tables.py
@@ -75,6 +75,11 @@ def _qualify(table: exp.Table) -> None:
                 _qualify(node)
 
     for scope in traverse_scope(expression):
+        for query in scope.subqueries:
+            subquery = query.parent
+            if isinstance(subquery, exp.Subquery):
+                subquery.unwrap().replace(subquery)
+
         for derived_table in scope.derived_tables:
             unnested = derived_table.unnest()
             if isinstance(unnested, exp.Table):
diff --git a/sqlglot/optimizer/scope.py b/sqlglot/optimizer/scope.py
index 96d3a60a1c..e3754db289 100644
--- a/sqlglot/optimizer/scope.py
+++ b/sqlglot/optimizer/scope.py
@@ -156,7 +156,7 @@ def _collect(self):
                 self._ctes.append(node)
             elif _is_derived_table(node) and _is_from_or_join(node):
                 self._derived_tables.append(node)
-            elif isinstance(node, exp.UNWRAPPED_QUERIES):
+            elif isinstance(node, exp.UNWRAPPED_QUERIES) and not _is_from_or_join(node):
                 self._subqueries.append(node)
             elif isinstance(node, exp.TableColumn):
                 self._table_columns.append(node)
@@ -821,7 +821,7 @@ def _traverse_udtfs(scope):
 
     sources = {}
     for expression in expressions:
-        if _is_derived_table(expression):
+        if isinstance(expression, exp.Subquery):
             top = None
             for child_scope in _traverse_scope(
                 scope.branch(
@@ -870,10 +870,7 @@ def walk_in_scope(expression, bfs=True, prune=None):
 
         if (
             isinstance(node, exp.CTE)
-            or (
-                isinstance(node.parent, (exp.From, exp.Join, exp.Subquery))
-                and _is_derived_table(node)
-            )
+            or (isinstance(node.parent, (exp.From, exp.Join)) and _is_derived_table(node))
             or (isinstance(node.parent, exp.UDTF) and isinstance(node, exp.Query))
             or isinstance(node, exp.UNWRAPPED_QUERIES)
         ):
diff --git a/tests/fixtures/optimizer/qualify_columns.sql b/tests/fixtures/optimizer/qualify_columns.sql
index 5b3b19bf4c..6676812a77 100644
--- a/tests/fixtures/optimizer/qualify_columns.sql
+++ b/tests/fixtures/optimizer/qualify_columns.sql
@@ -337,7 +337,7 @@ SELECT _q_0.a AS a FROM (SELECT x.a AS a FROM x AS x UNION SELECT x.a AS a FROM
 
 # title: nested subqueries in union
 ((select a from x where a < 1)) UNION ((select a from x where a > 2));
-((SELECT x.a AS a FROM x AS x WHERE x.a < 1)) UNION ((SELECT x.a AS a FROM x AS x WHERE x.a > 2));
+(SELECT x.a AS a FROM x AS x WHERE x.a < 1) UNION (SELECT x.a AS a FROM x AS x WHERE x.a > 2);
 
 
 # dialect: bigquery
@@ -443,6 +443,10 @@ SELECT _q_1.a AS a FROM (SELECT x.a AS a FROM x AS x) AS _q_1 WHERE _q_1.a IN (S
 SELECT * FROM table_a as A WHERE A.col1 IN (SELECT MAX(B.col2) FROM table_b as B UNION ALL SELECT MAX(C.col2) FROM table_b as C);
 SELECT * FROM table_a AS `A` WHERE `A`.col1 IN (SELECT MAX(`B`.col2) AS _col_0 FROM table_b AS `B` UNION ALL SELECT MAX(`C`.col2) AS _col_0 FROM table_b AS `C`);
 
+# Title: Unnest deep subquery
+select * from x where b in ((((select b from y))));
+SELECT x.a AS a, x.b AS b FROM x AS x WHERE x.b IN (SELECT y.b AS b FROM y AS y);
+
 --------------------------------------
 -- Correlated subqueries
 --------------------------------------