✨ feat(env): preserve existing env values

README.md

@@ -93,6 +93,22 @@ pytest --envfile .env.local           # ignore configured env_files, load only t
 pytest --envfile +.env.override       # load configured env_files first, then this file on top
 ```
 
+To keep existing environment variables (including with `--envfile`), set `env_files_skip_if_set = true`:
+
+```toml
+[tool.pytest_env]
+env_files = [".env", ".env.test"]
+env_files_skip_if_set = true
+```
+
+```ini
+[pytest]
+env_files =
+    .env
+    .env.test
+env_files_skip_if_set = true
+```
+
 ### Control variable behavior
 
 Variables set as plain values are assigned directly. For more control, use inline tables with the `transform`,
@@ -107,7 +123,8 @@ TEMP_VAR = { unset = true }
 ```
 
 `transform` expands `{VAR}` placeholders using existing environment variables. `skip_if_set` leaves the variable
-unchanged when it already exists. `unset` removes it entirely (different from setting to empty string).
+unchanged when it already exists. For `.env` files, use `env_files_skip_if_set = true`. `unset` removes it entirely
+(different from setting to empty string).
 
 ### Set different environments for test suites
 
@@ -253,7 +270,8 @@ When multiple sources define the same variable, precedence applies in this order
 1. Inline variables in configuration files (TOML or INI format).
 1. Variables from `.env` files loaded via `env_files`. When using `--envfile`, CLI files take precedence over
    configuration-based `env_files`.
-1. Variables already present in the environment (preserved when `skip_if_set = true` or `D:` flag is used).
+1. Variables already present in the environment (preserved when `skip_if_set = true`, `D:` flag is used, or
+   `env_files_skip_if_set = true`).
 
 When multiple configuration formats are present, TOML native format (`[pytest_env]` / `[tool.pytest_env]`) takes
 precedence over INI format. Among TOML files, the first file with a `pytest_env` section wins, checked in order:

pyproject.toml

@@ -2,7 +2,7 @@
 build-backend = "hatchling.build"
 requires = [
   "hatch-vcs>=0.5",
-  "hatchling>=1.28",
+  "hatchling>=1.29",
 ]
 
 [project]
@@ -38,7 +38,7 @@ dynamic = [
 ]
 dependencies = [
   "pytest>=9.0.2",
-  "python-dotenv>=1.2.1",
+  "python-dotenv>=1.2.2",
   "tomli>=2.4; python_version<'3.11'",
 ]
 optional-dependencies.testing = [

src/pytest_env/plugin.py

@@ -27,6 +27,12 @@ def pytest_addoption(parser: pytest.Parser) -> None:
     help_msg = "a line separated list of environment variables of the form (FLAG:)NAME=VALUE"
     parser.addini("env", type="linelist", help=help_msg, default=[])
     parser.addini("env_files", type="linelist", help="a line separated list of .env files to load", default=[])
+    parser.addini(
+        "env_files_skip_if_set",
+        type="bool",
+        help="only set .env file variables when not already defined",
+        default=False,
+    )
     parser.addoption(
         "--envfile",
         action="store",
@@ -65,10 +71,19 @@ def pytest_load_initial_conftests(
     actions: list[tuple[str, str, str, str]] = []
 
     env_files_list: list[str] = []
+    env_files_skip_if_set: bool | None = None
     if toml_config := _find_toml_config(early_config):
-        env_files_list, _ = _load_toml_config(toml_config)
+        env_files_list, _, env_files_skip_if_set = _load_toml_config(toml_config)
+
+    if env_files_skip_if_set is None:
+        env_files_skip_if_set = bool(early_config.getini("env_files_skip_if_set"))
 
-    _apply_env_files(early_config, env_files_list, actions if verbose else None)
+    _apply_env_files(
+        early_config,
+        env_files_list,
+        actions if verbose else None,
+        skip_if_set=env_files_skip_if_set,
+    )
     _apply_entries(early_config, actions if verbose else None)
 
     if verbose and actions:
@@ -79,13 +94,20 @@ def _apply_env_files(
     early_config: pytest.Config,
     env_files_list: list[str],
     actions: list[tuple[str, str, str, str]] | None,
+    *,
+    skip_if_set: bool = False,
 ) -> None:
+    preexisting = dict(os.environ) if skip_if_set else {}
     for env_file in _load_env_files(early_config, env_files_list):
         for key, value in dotenv_values(env_file).items():
             if value is not None:
-                os.environ[key] = value
-                if actions is not None:
-                    actions.append(("SET", key, value, str(env_file)))
+                if skip_if_set and key in preexisting:
+                    if actions is not None:
+                        actions.append(("SKIP", key, preexisting[key], str(env_file)))
+                else:
+                    os.environ[key] = value
+                    if actions is not None:
+                        actions.append(("SET", key, value, str(env_file)))
 
 
 def _apply_entries(
@@ -146,15 +168,15 @@ def _find_toml_config(early_config: pytest.Config) -> Path | None:
 def _config_source(early_config: pytest.Config) -> str:
     """Describe the configuration source for verbose output."""
     if toml_path := _find_toml_config(early_config):
-        _, entries = _load_toml_config(toml_path)
+        _, entries, _ = _load_toml_config(toml_path)
         if entries:
             return str(toml_path)
     if early_config.inipath:
         return str(early_config.inipath)
     return "config"  # pragma: no cover
 
 
-def _load_toml_config(config_path: Path) -> tuple[list[str], list[Entry]]:
+def _load_toml_config(config_path: Path) -> tuple[list[str], list[Entry], bool | None]:
     """Load env_files and entries from TOML config file."""
     with config_path.open("rb") as file_handler:
         config = tomllib.load(file_handler)
@@ -164,13 +186,15 @@ def _load_toml_config(config_path: Path) -> tuple[list[str], list[Entry]]:
 
     pytest_env_config = config.get("pytest_env", {})
     if not pytest_env_config:
-        return [], []
+        return [], [], None
 
     raw_env_files = pytest_env_config.get("env_files")
     env_files = [str(f) for f in raw_env_files] if isinstance(raw_env_files, list) else []
+    raw_skip = pytest_env_config.get("env_files_skip_if_set")
+    env_files_skip_if_set = raw_skip if isinstance(raw_skip, bool) else None
 
     entries = list(_parse_toml_config(pytest_env_config))
-    return env_files, entries
+    return env_files, entries, env_files_skip_if_set
 
 
 def _load_env_files(early_config: pytest.Config, env_files: list[str]) -> Generator[Path, None, None]:
@@ -199,7 +223,7 @@ def _load_env_files(early_config: pytest.Config, env_files: list[str]) -> Genera
 def _load_values(early_config: pytest.Config) -> Iterator[Entry]:
     """Load env entries from config, preferring TOML over INI."""
     if toml_config := _find_toml_config(early_config):
-        _, entries = _load_toml_config(toml_config)
+        _, entries, _ = _load_toml_config(toml_config)
         if entries:
             yield from entries
             return
@@ -224,6 +248,8 @@ def _parse_toml_config(config: dict[str, Any]) -> Generator[Entry, None, None]:
     for key, entry in config.items():
         if key == "env_files" and isinstance(entry, list):
             continue
+        if key == "env_files_skip_if_set" and isinstance(entry, bool):
+            continue
         if isinstance(entry, dict):
             unset = bool(entry.get("unset"))
             value = str(entry.get("value", "")) if not unset else ""

tests/test_env.py

@@ -408,6 +408,30 @@ def test_env_via_toml(  # noqa: PLR0913, PLR0917
             "pyproject",
             id="skip if set respects env file",
         ),
+        pytest.param(
+            {"MAGIC": "original"},
+            "MAGIC=from_file",
+            dedent("""\
+                [tool.pytest_env]
+                env_files = [".env"]
+                env_files_skip_if_set = true
+            """),
+            {"MAGIC": "original"},
+            "pyproject",
+            id="env_files_skip_if_set pyproject",
+        ),
+        pytest.param(
+            {"MAGIC": "original"},
+            "MAGIC=from_file",
+            dedent("""\
+                [pytest]
+                env_files = .env
+                env_files_skip_if_set = true
+            """),
+            {"MAGIC": "original"},
+            "ini",
+            id="env_files_skip_if_set ini",
+        ),
         pytest.param(
             {},
             "=no_key\nVALID=yes",
@@ -623,6 +647,31 @@ def test_envfile_cli(  # noqa: PLR0913, PLR0917
     result.assert_outcomes(passed=1)
 
 
+def test_envfile_cli_skip_if_set(pytester: pytest.Pytester) -> None:
+    (pytester.path / "test_cli_skip.py").symlink_to(Path(__file__).parent / "template.py")
+    (pytester.path / "cli.env").write_text("MAGIC=from_cli", encoding="utf-8")
+    (pytester.path / "pyproject.toml").write_text(
+        dedent("""\
+            [tool.pytest_env]
+            env_files_skip_if_set = true
+        """),
+        encoding="utf-8",
+    )
+
+    expected_env = {"MAGIC": "original"}
+    new_env = {
+        "MAGIC": "original",
+        "_TEST_ENV": repr(expected_env),
+        "PYTEST_DISABLE_PLUGIN_AUTOLOAD": "1",
+        "PYTEST_PLUGINS": "pytest_env.plugin",
+    }
+
+    with mock.patch.dict(os.environ, new_env, clear=True):
+        result = pytester.runpytest("--envfile", "cli.env")
+
+    result.assert_outcomes(passed=1)
+
+
 @pytest.mark.parametrize(
     "cli_arg",
     [

tests/test_verbose.py

@@ -89,6 +89,31 @@ def test_verbose_shows_set_from_env_file(pytester: pytest.Pytester) -> None:
     result.stdout.fnmatch_lines(["*SET*FROM_FILE=value*(from*.env*"])
 
 
+def test_verbose_shows_skip_from_env_file(pytester: pytest.Pytester) -> None:
+    (pytester.path / "test_it.py").symlink_to(Path(__file__).parent / "template.py")
+    (pytester.path / ".env").write_text("FROM_FILE=value", encoding="utf-8")
+    (pytester.path / "pyproject.toml").write_text(
+        dedent("""\
+            [tool.pytest_env]
+            env_files = [".env"]
+            env_files_skip_if_set = true
+        """),
+        encoding="utf-8",
+    )
+
+    new_env = {
+        "FROM_FILE": "original",
+        "_TEST_ENV": repr({"FROM_FILE": "original"}),
+        "PYTEST_DISABLE_PLUGIN_AUTOLOAD": "1",
+        "PYTEST_PLUGINS": "pytest_env.plugin",
+    }
+    with mock.patch.dict(os.environ, new_env, clear=True):
+        result = pytester.runpytest("--pytest-env-verbose")
+
+    result.assert_outcomes(passed=1)
+    result.stdout.fnmatch_lines(["*SKIP*FROM_FILE=original*(from*.env*"])
+
+
 def test_verbose_shows_skip(pytester: pytest.Pytester) -> None:
     (pytester.path / "test_it.py").symlink_to(Path(__file__).parent / "template.py")
     (pytester.path / "pytest.ini").write_text("[pytest]\nenv = D:EXISTING=new", encoding="utf-8")

tox.toml

@@ -1,3 +1,19 @@
+requires = [
+  "tox>=4.36.1",
+  "tox-uv>=1.29",
+]
+env_list = [
+  "3.14",
+  "3.13",
+  "3.12",
+  "3.11",
+  "3.10",
+  "fix",
+  "pkg_meta",
+  "type",
+]
+skip_missing_interpreters = true
+
 [env_run_base]
 description = "run the tests with pytest"
 package = "wheel"
@@ -22,19 +38,10 @@ commands = [
   [ "coverage", "html", "-d", "{envtmpdir}{/}htmlcov" ],
 ]
 
-[env.dev]
-description = "generate a DEV environment"
-package = "editable"
-extras = [ "testing" ]
-commands = [
-  [ "uv", "pip", "tree" ],
-  [ "python", "-c", "import sys; print(sys.executable)" ],
-]
-
 [env.fix]
 description = "run static analysis and style check using flake8"
 skip_install = true
-deps = [ "pre-commit-uv>=4.2" ]
+deps = [ "pre-commit-uv>=4.2.1" ]
 pass_env = [ "HOMEPATH", "PROGRAMDATA" ]
 commands = [ [ "pre-commit", "run", "--all-files", "--show-diff-on-failure" ] ]
 
@@ -44,7 +51,7 @@ skip_install = true
 deps = [
   "check-wheel-contents>=0.6.3",
   "twine>=6.2",
-  "uv>=0.10.3",
+  "uv>=0.10.9",
 ]
 commands = [
   [ "uv", "build", "--sdist", "--wheel", "--out-dir", "{env_tmp_dir}", "." ],
@@ -54,22 +61,14 @@ commands = [
 
 [env.type]
 description = "run type check on code base"
-deps = [ "ty==0.0.17" ]
+deps = [ "ty==0.0.22" ]
 commands = [ [ "ty", "check", "--output-format", "concise", "--error-on-warning", "." ] ]
 
-[tox]
-requires = [
-  "tox>=4.36.1",
-  "tox-uv>=1.29",
-]
-env_list = [
-  "fix",
-  "3.14",
-  "3.13",
-  "3.12",
-  "3.11",
-  "3.10",
-  "type",
-  "pkg_meta",
+[env.dev]
+description = "generate a DEV environment"
+package = "editable"
+extras = [ "testing" ]
+commands = [
+  [ "uv", "pip", "tree" ],
+  [ "python", "-c", "import sys; print(sys.executable)" ],
 ]
-skip_missing_interpreters = true