diff --git a/antarest/core/config.py b/antarest/core/config.py
index 1a93131a0a..db14a87c50 100644
--- a/antarest/core/config.py
+++ b/antarest/core/config.py
@@ -165,6 +165,8 @@ def from_dict(cls, data: JSON) -> "StorageConfig":
             if "workspaces" in data
             else defaults.workspaces
         )
+
+        cls._validate_workspaces(data, workspaces)
         return cls(
             matrixstore=Path(data["matrixstore"]) if "matrixstore" in data else defaults.matrixstore,
             archive_dir=Path(data["archive_dir"]) if "archive_dir" in data else defaults.archive_dir,
@@ -191,6 +193,19 @@ def from_dict(cls, data: JSON) -> "StorageConfig":
             ),
         )
 
+    @classmethod
+    def _validate_workspaces(cls, config_as_json: JSON, workspaces: Dict[str, WorkspaceConfig]) -> None:
+        """
+        Validate that no two workspaces have overlapping paths.
+        """
+        workspace_name_by_path = [(config.path, name) for name, config in workspaces.items()]
+        for path, name in workspace_name_by_path:
+            for path2, name2 in workspace_name_by_path:
+                if name != name2 and path.is_relative_to(path2):
+                    raise ValueError(
+                        f"Overlapping workspace paths found: '{name}' and '{name2}' '{path}' is relative to '{path2}' "
+                    )
+
 
 @dataclass(frozen=True)
 class NbCoresConfig:
diff --git a/antarest/study/service.py b/antarest/study/service.py
index 31bb80fa1f..9271e0dbdb 100644
--- a/antarest/study/service.py
+++ b/antarest/study/service.py
@@ -954,16 +954,17 @@ def sync_studies_on_disk(
                 all_studies = [raw_study for raw_study in all_studies if directory in Path(raw_study.path).parents]
             else:
                 all_studies = [raw_study for raw_study in all_studies if directory == Path(raw_study.path).parent]
-        studies_by_path = {study.path: study for study in all_studies}
+        studies_by_path_workspace = {(study.workspace, study.path): study for study in all_studies}
 
         # delete orphan studies on database
-        paths = [str(f.path) for f in folders]
+        # key should be workspace, path to sync correctly studies with same path in different workspace
+        workspace_paths = [(f.workspace, str(f.path)) for f in folders]
 
         for study in all_studies:
             if (
                 isinstance(study, RawStudy)
                 and not study.archived
-                and (study.workspace != DEFAULT_WORKSPACE_NAME and study.path not in paths)
+                and (study.workspace != DEFAULT_WORKSPACE_NAME and (study.workspace, study.path) not in workspace_paths)
             ):
                 if not study.missing:
                     logger.info(
@@ -990,11 +991,12 @@ def sync_studies_on_disk(
                     self.repository.delete(study.id)
 
         # Add new studies
-        study_paths = [study.path for study in all_studies if study.missing is None]
+        study_paths = [(study.workspace, study.path) for study in all_studies if study.missing is None]
         missing_studies = {study.path: study for study in all_studies if study.missing is not None}
         for folder in folders:
             study_path = str(folder.path)
-            if study_path not in study_paths:
+            workspace = folder.workspace
+            if (workspace, study_path) not in study_paths:
                 try:
                     if study_path not in missing_studies.keys():
                         base_path = self.config.storage.workspaces[folder.workspace].path
@@ -1004,7 +1006,7 @@ def sync_studies_on_disk(
                             name=folder.path.name,
                             path=study_path,
                             folder=str(dir_name),
-                            workspace=folder.workspace,
+                            workspace=workspace,
                             owner=None,
                             groups=folder.groups,
                             public_mode=PublicMode.FULL if len(folder.groups) == 0 else PublicMode.NONE,
@@ -1039,8 +1041,8 @@ def sync_studies_on_disk(
                     )
                 except Exception as e:
                     logger.error(f"Failed to add study {folder.path}", exc_info=e)
-            elif directory and study_path in studies_by_path:
-                existing_study = studies_by_path[study_path]
+            elif directory and (workspace, study_path) in studies_by_path_workspace:
+                existing_study = studies_by_path_workspace[(workspace, study_path)]
                 if self.storage_service.raw_study_service.update_name_and_version_from_raw_meta(existing_study):
                     self.repository.save(existing_study)
 
diff --git a/tests/storage/test_config.py b/tests/storage/test_config.py
new file mode 100644
index 0000000000..9e7dc8ec47
--- /dev/null
+++ b/tests/storage/test_config.py
@@ -0,0 +1,103 @@
+from pathlib import Path
+
+import pytest
+
+from antarest.core.config import InternalMatrixFormat, StorageConfig
+
+
+@pytest.fixture
+def storage_config_default():
+    return {
+        "matrixstore": "./custom_matrixstore",
+        "archive_dir": "./custom_archives",
+        "tmp_dir": "./custom_tmp",
+        "allow_deletion": True,
+        "watcher_lock": False,
+        "watcher_lock_delay": 20,
+        "download_default_expiration_timeout_minutes": 2880,
+        "matrix_gc_sleeping_time": 7200,
+        "matrix_gc_dry_run": True,
+        "auto_archive_threshold_days": 120,
+        "auto_archive_dry_run": True,
+        "auto_archive_sleeping_time": 7200,
+        "auto_archive_max_parallel": 10,
+        "snapshot_retention_days": 14,
+        "matrixstore_format": "tsv",
+    }
+
+
+def test_storage_config_from_dict(storage_config_default):
+    data = {
+        **storage_config_default,
+        "workspaces": {
+            "workspace1": {
+                "path": "./workspace1",
+            },
+            "workspace2": {
+                "path": "./workspace2",
+            },
+        },
+    }
+
+    config = StorageConfig.from_dict(data)
+
+    assert config.matrixstore == Path("./custom_matrixstore")
+    assert config.archive_dir == Path("./custom_archives")
+    assert config.tmp_dir == Path("./custom_tmp")
+    assert config.workspaces["workspace1"].path == Path("./workspace1")
+    assert config.workspaces["workspace2"].path == Path("./workspace2")
+    assert config.allow_deletion is True
+    assert config.watcher_lock is False
+    assert config.watcher_lock_delay == 20
+    assert config.download_default_expiration_timeout_minutes == 2880
+    assert config.matrix_gc_sleeping_time == 7200
+    assert config.matrix_gc_dry_run is True
+    assert config.auto_archive_threshold_days == 120
+    assert config.auto_archive_dry_run is True
+    assert config.auto_archive_sleeping_time == 7200
+    assert config.auto_archive_max_parallel == 10
+    assert config.snapshot_retention_days == 14
+    assert config.matrixstore_format == InternalMatrixFormat.TSV
+
+
+def test_storage_config_from_dict_validiation_errors(storage_config_default):
+    data = {
+        **storage_config_default,
+        "workspaces": {
+            "workspace1": {
+                "path": "./a/workspace1",
+            },
+            "workspace2": {
+                "path": "./a/",
+            },
+        },
+    }
+
+    with pytest.raises(ValueError):
+        StorageConfig.from_dict(data)
+
+    data = {
+        **storage_config_default,
+        "workspaces": {
+            "workspace1": {
+                "path": "./a/",
+            },
+            "workspace2": {
+                "path": "./a/workspace2",
+            },
+        },
+    }
+
+    with pytest.raises(ValueError):
+        StorageConfig.from_dict(data)
+
+    data = {
+        **storage_config_default,
+        "workspaces": {
+            "workspace1": {"path": "./a/", "some_other_config": "value1"},
+            "workspace2": {"path": "./a/", "some_other_config": "value2"},
+        },
+    }
+
+    with pytest.raises(ValueError):
+        StorageConfig.from_dict(data)
diff --git a/tests/storage/test_service.py b/tests/storage/test_service.py
index 06a7d45b0f..bd860d1ba9 100644
--- a/tests/storage/test_service.py
+++ b/tests/storage/test_service.py
@@ -259,8 +259,8 @@ def test_study_listing(db_session: Session) -> None:
 @pytest.mark.unit_test
 def test_sync_studies_from_disk() -> None:
     now = datetime.utcnow()
-    ma = RawStudy(id="a", path="a")
-    fa = StudyFolder(path=Path("a"), workspace="", groups=[])
+    ma = RawStudy(id="a", path="a", workspace="workspace1")
+    fa = StudyFolder(path=Path("a"), workspace="workspace1", groups=[])
     mb = RawStudy(id="b", path="b")
     mc = RawStudy(
         id="c",