diff --git a/docs/docs/usage/scripts.md b/docs/docs/usage/scripts.md
index 0a93faa4ef..4dd61794ab 100644
--- a/docs/docs/usage/scripts.md
+++ b/docs/docs/usage/scripts.md
@@ -146,6 +146,15 @@ start.cmd = "flask run -p 54321"
 start.env_file = ".env"
 ```
 
+The variables within the dotenv file will *not* override any existing environment variables.
+If you want the dotenv file to override existing environment variables use the following:
+
+```toml
+[tool.pdm.scripts]
+start.cmd = "flask run -p 54321"
+start.env_file.override = ".env"
+```
+
 !!! note
     A dotenv file specified on a composite task level will override those defined by called tasks.
 
diff --git a/news/1299.feature b/news/1299.feature
new file mode 100644
index 0000000000..ce9bd61132
--- /dev/null
+++ b/news/1299.feature
@@ -0,0 +1,4 @@
+Add a env_file.override option that allows the user to specify that
+the env_file should override any existing environment variables. This
+is not the default as the environment the code runs it should take
+precedence.
diff --git a/pdm/cli/commands/run.py b/pdm/cli/commands/run.py
index c8586c7c57..4fcf677c55 100644
--- a/pdm/cli/commands/run.py
+++ b/pdm/cli/commands/run.py
@@ -21,9 +21,13 @@
 from pdm.utils import is_path_relative_to
 
 
+class EnvFileOptions(TypedDict, total=True):
+    override: str
+
+
 class TaskOptions(TypedDict, total=False):
     env: Mapping[str, str]
-    env_file: str | None
+    env_file: EnvFileOptions | str | None
     help: str
     site_packages: bool
 
@@ -119,12 +123,19 @@ def _run_process(
         shell: bool = False,
         site_packages: bool = False,
         env: Mapping[str, str] | None = None,
-        env_file: str | None = None,
+        env_file: EnvFileOptions | str | None = None,
     ) -> int:
         """Run command in a subprocess and return the exit code."""
         project = self.project
-        process_env = {}
-        if env_file:
+        process_env = os.environ.copy()
+        if env_file is not None:
+            if isinstance(env_file, str):
+                path = env_file
+                override = False
+            else:
+                path = env_file["override"]
+                override = True
+
             import dotenv
 
             project.core.ui.echo(
@@ -132,10 +143,11 @@ def _run_process(
                 err=True,
                 verbosity=termui.Verbosity.DETAIL,
             )
-            process_env = dotenv.dotenv_values(
-                project.root / env_file, encoding="utf-8"
-            )
-        process_env.update(os.environ)
+            dotenv_env = dotenv.dotenv_values(project.root / path, encoding="utf-8")
+            if override:
+                process_env = {**process_env, **dotenv_env}
+            else:
+                process_env = {**dotenv_env, **process_env}
         pythonpath = process_env.get("PYTHONPATH", "").split(os.pathsep)
         pythonpath = [PEP582_PATH] + [
             p for p in pythonpath if "pdm/pep582" not in p.replace("\\", "/")
diff --git a/tests/cli/test_run.py b/tests/cli/test_run.py
index 0943b8a8a2..f95a75e830 100644
--- a/tests/cli/test_run.py
+++ b/tests/cli/test_run.py
@@ -230,20 +230,26 @@ def test_run_script_with_env_defined(project, invoke, capfd):
         assert capfd.readouterr()[0].strip() == "bar"
 
 
-def test_run_script_with_dotenv_file(project, invoke, capfd):
+def test_run_script_with_dotenv_file(project, invoke, capfd, monkeypatch):
     (project.root / "test_script.py").write_text(
         "import os; print(os.getenv('FOO'), os.getenv('BAR'))"
     )
     project.tool_settings["scripts"] = {
-        "_": {"env": {"BAR": "foo"}},
-        "test_script": {"cmd": "python test_script.py", "env_file": ".env"},
+        "test_override": {
+            "cmd": "python test_script.py",
+            "env_file": {"override": ".env"},
+        },
+        "test_default": {"cmd": "python test_script.py", "env_file": ".env"},
     }
     project.write_pyproject()
+    monkeypatch.setenv("BAR", "foo")
     (project.root / ".env").write_text("FOO=bar\nBAR=override")
     capfd.readouterr()
     with cd(project.root):
-        invoke(["run", "test_script"], obj=project)
+        invoke(["run", "test_default"], obj=project)
         assert capfd.readouterr()[0].strip() == "bar foo"
+        invoke(["run", "test_override"], obj=project)
+        assert capfd.readouterr()[0].strip() == "bar override"
 
 
 def test_run_script_override_global_env(project, invoke, capfd):