diff --git a/gns3server/modules/base_manager.py b/gns3server/modules/base_manager.py
index 641ed790..aef1579a 100644
--- a/gns3server/modules/base_manager.py
+++ b/gns3server/modules/base_manager.py
@@ -142,6 +142,7 @@ class BaseManager:
             uuid = str(uuid4())
 
         vm = self._VM_CLASS(name, uuid, project, self, *args, **kwargs)
+        project.add_vm(vm)
         if asyncio.iscoroutinefunction(vm.create):
             yield from vm.create()
         else:
diff --git a/gns3server/modules/base_vm.py b/gns3server/modules/base_vm.py
index 42deb98f..52c003b2 100644
--- a/gns3server/modules/base_vm.py
+++ b/gns3server/modules/base_vm.py
@@ -27,7 +27,6 @@ class BaseVM:
         self._uuid = uuid
         self._project = project
         self._manager = manager
-        project.add_vm(self)
 
         log.debug("{module}: {name} [{uuid}] initialized".format(module=self.manager.module_name,
                                                                  name=self.name,
diff --git a/gns3server/modules/project.py b/gns3server/modules/project.py
index a3e0319f..4e8c61df 100644
--- a/gns3server/modules/project.py
+++ b/gns3server/modules/project.py
@@ -95,6 +95,7 @@ class Project:
         :param vm: An instance of VM
         """
 
+        self.remove_vm(vm)
         self._vms_to_destroy.add(vm)
 
     def __json__(self):
@@ -106,14 +107,25 @@ class Project:
 
     def add_vm(self, vm):
         """
-        Add a VM to the project. In theory this should be called by
-        the VM initializer.
+        Add a VM to the project.
+        In theory this should be called by the VM manager.
 
         :params vm: A VM instance
         """
 
         self._vms.add(vm)
 
+    def remove_vm(self, vm):
+        """
+        Remove a VM from the project.
+        In theory this should be called by the VM manager.
+
+        :params vm: A VM instance
+        """
+
+        if vm in self._vms:
+            self._vms.remove(vm)
+
     def close(self):
         """Close the project, but keep informations on disk"""
 
@@ -128,6 +140,7 @@ class Project:
             directory = self.vm_working_directory(vm)
             if os.path.exists(directory):
                 shutil.rmtree(directory)
+            self.remove_vm(vm)
 
     def delete(self):
         """Remove project from disk"""
diff --git a/tests/modules/test_project.py b/tests/modules/test_project.py
index 2956adaf..d26488ac 100644
--- a/tests/modules/test_project.py
+++ b/tests/modules/test_project.py
@@ -68,14 +68,17 @@ def test_vm_working_directory(tmpdir, vm):
 
 
 def test_mark_vm_for_destruction(tmpdir, vm):
-    p = Project(location=str(tmpdir))
-    p.mark_vm_for_destruction(vm)
-    assert len(p._vms_to_destroy) == 1
+    project = Project(location=str(tmpdir))
+    project.add_vm(vm)
+    project.mark_vm_for_destruction(vm)
+    assert len(project._vms_to_destroy) == 1
+    assert len(project.vms) == 0
 
 
 def test_commit(tmpdir, manager):
     project = Project(location=str(tmpdir))
     vm = VPCSVM("test", "00010203-0405-0607-0809-0a0b0c0d0e0f", project, manager)
+    project.add_vm(vm)
     directory = project.vm_working_directory(vm)
     project.mark_vm_for_destruction(vm)
     assert len(project._vms_to_destroy) == 1
@@ -83,6 +86,7 @@ def test_commit(tmpdir, manager):
     project.commit()
     assert len(project._vms_to_destroy) == 0
     assert os.path.exists(directory) is False
+    assert len(project.vms) == 0
 
 
 def test_project_delete(tmpdir):
@@ -95,8 +99,8 @@ def test_project_delete(tmpdir):
 
 def test_project_add_vm(tmpdir, manager):
     project = Project(location=str(tmpdir))
-    # The VM initalizer call the add_vm method
     vm = VPCSVM("test", "00010203-0405-0607-0809-0a0b0c0d0e0f", project, manager)
+    project.add_vm(vm)
     assert len(project.vms) == 1