diff --git a/loki/program_unit.py b/loki/program_unit.py
index 11877e8ce..798fa0480 100644
--- a/loki/program_unit.py
+++ b/loki/program_unit.py
@@ -290,12 +290,13 @@ def clone(self, **kwargs):
         kwargs.setdefault('incomplete', self._incomplete)
 
         # Rebuild IRs
+        rebuild = Transformer({}, rebuild_scopes=True)
         if 'docstring' in kwargs:
-            kwargs['docstring'] = Transformer({}).visit(kwargs['docstring'])
+            kwargs['docstring'] = rebuild.visit(kwargs['docstring'])
         if 'spec' in kwargs:
-            kwargs['spec'] = Transformer({}).visit(kwargs['spec'])
+            kwargs['spec'] = rebuild.visit(kwargs['spec'])
         if 'contains' in kwargs:
-            kwargs['contains'] = Transformer({}).visit(kwargs['contains'])
+            kwargs['contains'] = rebuild.visit(kwargs['contains'])
 
         # Rescope symbols if not explicitly disabled
         kwargs.setdefault('rescope_symbols', True)
diff --git a/loki/subroutine.py b/loki/subroutine.py
index bdf56fc2c..55260afa6 100644
--- a/loki/subroutine.py
+++ b/loki/subroutine.py
@@ -288,7 +288,7 @@ def clone(self, **kwargs):
 
         # Rebuild body (other IR components are taken care of in super class)
         if 'body' in kwargs:
-            kwargs['body'] = Transformer({}).visit(kwargs['body'])
+            kwargs['body'] = Transformer({}, rebuild_scopes=True).visit(kwargs['body'])
 
         # Escalate to parent class
         return super().clone(**kwargs)
diff --git a/tests/test_modules.py b/tests/test_modules.py
index 55a21f3e1..bbb52726d 100644
--- a/tests/test_modules.py
+++ b/tests/test_modules.py
@@ -13,7 +13,7 @@
     OFP, OMNI, Module, Subroutine, VariableDeclaration, TypeDef, fexprgen,
     BasicType, Assignment, FindNodes, FindInlineCalls, FindTypedSymbols,
     Transformer, fgen, SymbolAttributes, Variable, Import, Section, Intrinsic,
-    Scalar, DeferredTypeSymbol
+    Scalar, DeferredTypeSymbol, FindVariables, SubstituteExpressions, Literal
 )
 
 
@@ -529,6 +529,55 @@ def test_module_rescope_clone(frontend):
     with pytest.raises(AttributeError):
         fgen(other_module_copy)
 
+@pytest.mark.parametrize('frontend', available_frontends(
+    xfail=[(OMNI, 'Parsing fails without dummy module provided')]
+))
+def test_module_deep_clone(frontend):
+    """
+    Test the rescoping of variables in clone with nested scopes.
+    """
+    fcode = """
+module test_module_rescope_clone
+  use parkind1, only : jpim, jprb
+  implicit none
+
+  integer :: n
+
+  real :: array(n)
+
+  type my_type
+    real :: vector(n)
+    real :: matrix(n, n)
+  end type
+
+end module test_module_rescope_clone
+"""
+    module = Module.from_source(fcode, frontend=frontend)
+
+    # Deep-copy/clone the module
+    new_module = module.clone()
+
+    n = [v for v in FindVariables().visit(new_module.spec) if v.name == 'n'][0]
+    n_decl = FindNodes(VariableDeclaration).visit(new_module.spec)[0]
+
+    # Remove the declaration of `n` and replace it with `3`
+    new_module.spec = Transformer({n_decl: None}).visit(new_module.spec)
+    new_module.spec = SubstituteExpressions({n: Literal(3)}).visit(new_module.spec)
+
+    # Check the new module has been changed
+    assert len(FindNodes(VariableDeclaration).visit(new_module.spec)) == 1
+    new_type_decls = FindNodes(VariableDeclaration).visit(new_module['my_type'].body)
+    assert len(new_type_decls) == 2
+    assert new_type_decls[0].symbols[0] == 'vector(3)'
+    assert new_type_decls[1].symbols[0] == 'matrix(3, 3)'
+
+    # Check the old one has not changed
+    assert len(FindNodes(VariableDeclaration).visit(module.spec)) == 2
+    type_decls = FindNodes(VariableDeclaration).visit(module['my_type'].body)
+    assert len(type_decls) == 2
+    assert type_decls[0].symbols[0] == 'vector(n)'
+    assert type_decls[1].symbols[0] == 'matrix(n, n)'
+
 
 @pytest.mark.parametrize('frontend', available_frontends())
 def test_module_access_spec_none(frontend):
diff --git a/tests/test_subroutine.py b/tests/test_subroutine.py
index d126d295d..f6df24a24 100644
--- a/tests/test_subroutine.py
+++ b/tests/test_subroutine.py
@@ -2054,3 +2054,48 @@ def test_enrich_calls_explicit_interface(frontend):
     # confirm that rescoping symbols has no effect
     driver.rescope_symbols()
     assert calls[0].routine is kernel
+
+
+@pytest.mark.parametrize('frontend', available_frontends(
+    xfail=[(OMNI, 'OMNI cannot handle external type defs without source')]
+))
+def test_subroutine_deep_clone(frontend):
+    """
+    Test that deep-cloning a subroutine actually ensures clean scope separation.
+    """
+
+    fcode = """
+subroutine myroutine(something)
+  use parkind1, only : jpim, jprb
+  implicit none
+
+  type(that_thing), intent(inout) :: something
+  real(kind=jprb) :: foo(something%n)
+
+  foo(:)=0.0_jprb
+
+  associate(thing=>something%else)
+    if (something%entirely%different) then
+      foo(:)=42.0_jprb
+    else
+      foo(:)=66.6_jprb
+    end if
+  end associate
+end subroutine myroutine
+"""
+    routine = Subroutine.from_source(fcode, frontend=frontend)
+
+    # Create a deep-copy of the routine
+    new_routine = routine.clone()
+
+    # Replace all assignments with dummy calls
+    map_nodes={}
+    for assign in FindNodes(Assignment).visit(new_routine.body):
+        map_nodes[assign] = CallStatement(
+            name=DeferredTypeSymbol(name='testcall'), arguments=(assign.lhs,), scope=new_routine
+        )
+    new_routine.body = Transformer(map_nodes).visit(new_routine.body)
+
+    # Ensure that the original copy of the routine remains unaffected
+    assert len(FindNodes(Assignment).visit(routine.body)) == 3
+    assert len(FindNodes(Assignment).visit(new_routine.body)) == 0