diff --git a/docs/home/migration.md b/docs/home/migration.md
index 9fafa6f9a..8c76cfd91 100644
--- a/docs/home/migration.md
+++ b/docs/home/migration.md
@@ -33,6 +33,35 @@ from bloqade.analog.atom_arrangement import Square
 ...
 ```
 
+## Migrating old bloqade JSON files
+
+If you have old bloqade JSON files, you will not be able to directly deserialize them anymore because of the package restructuring. However, we have provided some tools to migrate those JSON files to be compatible with `bloqade-analog`. You can do this by running the following command in the command line for a one or more files:
+
+```sh
+python -m bloqade.analog.migrate <path_to_old_json_file1> <path_to_old_json_file2> ...
+```
+With default arguments this will create a new file with the same name as the old file, but with `-analog` appended to the end of the filename. For example, if you have a file called `my_bloqade.json`, the new file will be called `my_bloqade-analog.json`. You can then use `load` to deserialize this file with the `bloqade-analog` package. There are other options for converting the file, such as setting the indent level for the output file or overwriting the old file. You can see all the options by running:
+
+```sh
+python -m bloqade.analog.migrate --help
+```
+
+Another option is to use the migration tool in a python script:
+
+```python
+from bloqade.analog.migrate import migrate
+
+ # set the indent level for the output file
+indent: int = ...
+# set to True if you want to overwrite the old file, otherwise the new file will be created with -analog appended to the end of the filename
+overwrite: bool = ...
+f
+or filename in ["file1.json", "file2.json", ...]:
+    migrate(filename, indent=indent, overwrite=overwrite)
+```
+This will migrate all the files in the list to the new format.
+
+
 ## Having trouble, comments, or concerns?
 
 Please open an issue on our [GitHub](https://github.com/QuEraComputing/bloqade-analog/issues)
diff --git a/src/bloqade/analog/migrate.py b/src/bloqade/analog/migrate.py
new file mode 100644
index 000000000..beaf88919
--- /dev/null
+++ b/src/bloqade/analog/migrate.py
@@ -0,0 +1,79 @@
+from typing import IO, Any, Dict, List
+from dataclasses import field, dataclass
+
+import simplejson as json
+
+
+@dataclass
+class JSONWalker:
+    has_done_something: bool = field(init=False, default=False)
+
+    def walk_dict(self, obj: Dict[str, Any]) -> Dict[str, Any]:
+        new_obj = {}
+        for key, value in obj.items():
+
+            if key.startswith("bloqade.analog."):
+                new_obj[key] = self.walk(value)
+            elif key.startswith("bloqade."):
+                new_obj[key.replace("bloqade.", "bloqade.analog.")] = self.walk(value)
+                self.has_done_something = True
+            else:
+                new_obj[key] = self.walk(value)
+
+        return new_obj
+
+    def walk(self, obj: Dict[str, Any] | List[Any]) -> Dict[str, Any] | List[Any]:
+        if isinstance(obj, dict):
+            return self.walk_dict(obj)
+        elif isinstance(obj, list):
+            return list(map(self.walk, obj))
+        else:
+            return obj
+
+    def convert(self, obj: Dict[str, Any] | List[Any]):
+        self.has_done_something = False
+        new_obj = self.walk(obj)
+        return new_obj, self.has_done_something
+
+
+def _migrate(input_oi: IO[str], output_oi: IO[str], indent: int | None = None):
+    obj = json.load(input_oi)
+    new_obj, has_done_something = JSONWalker().convert(obj)
+
+    if has_done_something:
+        json.dump(new_obj, output_oi, indent=indent)
+
+
+def migrate(
+    filename: str,
+    indent: int | None = None,
+    overwrite: bool = False,
+):
+    new_filename = filename if overwrite else filename.replace(".json", "-analog.json")
+    with open(filename, "r") as in_io, open(new_filename, "w") as out_io:
+        _migrate(in_io, out_io, indent)
+
+
+def _entry():
+    import argparse
+
+    import tqdm
+
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument("filenames", type=str, nargs="*")
+    parser.add_argument("--indent", type=int, default=None)
+    parser.add_argument(
+        "--overwrite",
+        action="store_true",
+        help="Overwrite the original file",
+        default=False,
+    )
+
+    args = parser.parse_args()
+    for filename in tqdm.tqdm(args.filenames):
+        migrate(filename, args.indent, args.overwrite)
+
+
+if __name__ == "__main__":
+    _entry()
diff --git a/tests/test_migrate.py b/tests/test_migrate.py
new file mode 100644
index 000000000..d710aabc1
--- /dev/null
+++ b/tests/test_migrate.py
@@ -0,0 +1,34 @@
+import io
+
+import simplejson as json
+
+from bloqade.analog.migrate import _migrate
+
+
+def test_walk_dict():
+
+    obj = {
+        "key1": "value1",
+        "bloqade.key2": "value2",
+        "bloqade.analog.key3": "value3",
+        "nested": {"key4": "bloqade.value4", "bloqade.key5": "value5"},
+        "list": [{"key6": "value6"}, {"bloqade.key7": "value7"}],
+    }
+
+    expected = {
+        "key1": "value1",
+        "bloqade.analog.key2": "value2",
+        "bloqade.analog.key3": "value3",
+        "nested": {"key4": "bloqade.value4", "bloqade.analog.key5": "value5"},
+        "list": [{"key6": "value6"}, {"bloqade.analog.key7": "value7"}],
+    }
+
+    obj_str = json.dumps(obj)
+    expected_str = json.dumps(expected)
+
+    in_io = io.StringIO(obj_str)
+    out_io = io.StringIO()
+
+    _migrate(in_io, out_io)
+
+    assert out_io.getvalue() == expected_str