diff --git a/doc/whatsnew/fragments/3696.breaking b/doc/whatsnew/fragments/3696.breaking
new file mode 100644
index 0000000000..ad93e45098
--- /dev/null
+++ b/doc/whatsnew/fragments/3696.breaking
@@ -0,0 +1,13 @@
+Enabling or disabling individual messages will now take effect even if an
+``--enable=all`` or ``disable=all`` follows in the same configuration file
+(or on the command line).
+
+This means for the following example, ``fixme`` messages will now be emitted::
+
+.. code-block::
+
+    pylint my_module --enable=fixme --disable=all
+
+To regain the prior behavior, remove the superfluous earlier option.
+
+Closes #3696
diff --git a/pylint/config/config_initialization.py b/pylint/config/config_initialization.py
index 85602197e5..514bdcd815 100644
--- a/pylint/config/config_initialization.py
+++ b/pylint/config/config_initialization.py
@@ -13,7 +13,10 @@
 
 from pylint import reporters
 from pylint.config.config_file_parser import _ConfigurationFileParser
-from pylint.config.exceptions import _UnrecognizedOptionError
+from pylint.config.exceptions import (
+    ArgumentPreprocessingError,
+    _UnrecognizedOptionError,
+)
 from pylint.utils import utils
 
 if TYPE_CHECKING:
@@ -46,6 +49,9 @@ def _config_initialization(
         print(ex, file=sys.stderr)
         sys.exit(32)
 
+    # Order --enable=all or --disable=all to come first.
+    config_args = _order_all_first(config_args, joined=False)
+
     # Run init hook, if present, before loading plugins
     if "init-hook" in config_data:
         exec(utils._unquote(config_data["init-hook"]))  # pylint: disable=exec-used
@@ -73,6 +79,7 @@ def _config_initialization(
 
     # Now we parse any options from the command line, so they can override
     # the configuration file
+    args_list = _order_all_first(args_list, joined=True)
     parsed_args_list = linter._parse_command_line_configuration(args_list)
 
     # Remove the positional arguments separator from the list of arguments if it exists
@@ -147,3 +154,48 @@ def _config_initialization(
             for arg in parsed_args_list
         )
     )
+
+
+def _order_all_first(config_args: list[str], *, joined: bool) -> list[str]:
+    """Reorder config_args such that --enable=all or --disable=all comes first.
+
+    Raise if both are given.
+
+    If joined is True, expect args in the form '--enable=all,for-any-all'.
+    If joined is False, expect args in the form '--enable', 'all,for-any-all'.
+    """
+    indexes_to_prepend = []
+    all_action = ""
+
+    for i, arg in enumerate(config_args):
+        if joined and (arg.startswith("--enable=") or arg.startswith("--disable=")):
+            value = arg.split("=")[1]
+        elif arg in {"--enable", "--disable"}:
+            value = config_args[i + 1]
+        else:
+            continue
+
+        if "all" not in (msg.strip() for msg in value.split(",")):
+            continue
+
+        arg = arg.split("=")[0]
+        if all_action and (arg != all_action):
+            raise ArgumentPreprocessingError(
+                "--enable=all and --disable=all are incompatible."
+            )
+        all_action = arg
+
+        indexes_to_prepend.append(i)
+        if not joined:
+            indexes_to_prepend.append(i + 1)
+
+    returned_args = []
+    for i in indexes_to_prepend:
+        returned_args.append(config_args[i])
+
+    for i, arg in enumerate(config_args):
+        if i in indexes_to_prepend:
+            continue
+        returned_args.append(arg)
+
+    return returned_args
diff --git a/tests/config/functional/toml/toml_with_mutually_exclusive_disable_enable_all.toml b/tests/config/functional/toml/toml_with_mutually_exclusive_disable_enable_all.toml
new file mode 100644
index 0000000000..9b422d8b7a
--- /dev/null
+++ b/tests/config/functional/toml/toml_with_mutually_exclusive_disable_enable_all.toml
@@ -0,0 +1,3 @@
+[tool.pylint."messages control"]
+disable = "all"
+enable = "all"
diff --git a/tests/config/functional/toml/toml_with_specific_disable_before_enable_all.toml b/tests/config/functional/toml/toml_with_specific_disable_before_enable_all.toml
new file mode 100644
index 0000000000..120132a30a
--- /dev/null
+++ b/tests/config/functional/toml/toml_with_specific_disable_before_enable_all.toml
@@ -0,0 +1,3 @@
+[tool.pylint."messages control"]
+disable = "fixme"
+enable = "all"
diff --git a/tests/config/functional/toml/toml_with_specific_enable_before_disable_all.toml b/tests/config/functional/toml/toml_with_specific_enable_before_disable_all.toml
new file mode 100644
index 0000000000..539597cc58
--- /dev/null
+++ b/tests/config/functional/toml/toml_with_specific_enable_before_disable_all.toml
@@ -0,0 +1,3 @@
+[tool.pylint."messages control"]
+enable = "fixme"
+disable = "all"
diff --git a/tests/config/test_config.py b/tests/config/test_config.py
index ff49d901ec..83c8b072e5 100644
--- a/tests/config/test_config.py
+++ b/tests/config/test_config.py
@@ -11,6 +11,7 @@
 import pytest
 from pytest import CaptureFixture
 
+from pylint.config.exceptions import ArgumentPreprocessingError
 from pylint.interfaces import CONFIDENCE_LEVEL_NAMES
 from pylint.lint import Run as LintRun
 from pylint.testutils import create_files
@@ -20,6 +21,7 @@
 HERE = Path(__file__).parent.absolute()
 REGRTEST_DATA_DIR = HERE / ".." / "regrtest_data"
 EMPTY_MODULE = REGRTEST_DATA_DIR / "empty.py"
+FIXME_MODULE = REGRTEST_DATA_DIR / "fixme.py"
 
 
 def check_configuration_file_reader(
@@ -175,3 +177,45 @@ def test_clear_cache_post_run() -> None:
 
     assert not run_before_edit.linter.stats.by_msg
     assert run_after_edit.linter.stats.by_msg
+
+
+def test_enable_all_disable_all_mutually_exclusive() -> None:
+    with pytest.raises(ArgumentPreprocessingError):
+        runner = Run(["--enable=all", "--disable=all", str(EMPTY_MODULE)], exit=False)
+
+    runner = Run(["--enable=all", "--enable=all", str(EMPTY_MODULE)], exit=False)
+    assert not runner.linter.stats.by_msg
+
+    with pytest.raises(ArgumentPreprocessingError):
+        run_using_a_configuration_file(
+            HERE
+            / "functional"
+            / "toml"
+            / "toml_with_mutually_exclusive_disable_enable_all.toml",
+        )
+
+
+def test_disable_before_enable_all_takes_effect() -> None:
+    runner = Run(["--disable=fixme", "--enable=all", str(FIXME_MODULE)], exit=False)
+    assert not runner.linter.stats.by_msg
+
+    _, _, toml_runner = run_using_a_configuration_file(
+        HERE
+        / "functional"
+        / "toml"
+        / "toml_with_specific_disable_before_enable_all.toml",
+    )
+    assert not toml_runner.linter.is_message_enabled("fixme")
+
+
+def test_enable_before_disable_all_takes_effect() -> None:
+    runner = Run(["--enable=fixme", "--disable=all", str(FIXME_MODULE)], exit=False)
+    assert runner.linter.stats.by_msg
+
+    _, _, toml_runner = run_using_a_configuration_file(
+        HERE
+        / "functional"
+        / "toml"
+        / "toml_with_specific_enable_before_disable_all.toml",
+    )
+    assert toml_runner.linter.is_message_enabled("fixme")
diff --git a/tests/config/test_functional_config_loading.py b/tests/config/test_functional_config_loading.py
index 0bbfe50ff6..0bce30701b 100644
--- a/tests/config/test_functional_config_loading.py
+++ b/tests/config/test_functional_config_loading.py
@@ -43,6 +43,11 @@
     str(path.relative_to(FUNCTIONAL_DIR))
     for ext in ACCEPTED_CONFIGURATION_EXTENSIONS
     for path in FUNCTIONAL_DIR.rglob(f"*.{ext}")
+    if (str_path := str(path))
+    # The enable/disable all tests are not practical with this framework.
+    # They require manually listing ~400 messages, which will
+    # require constant updates.
+    and "enable_all" not in str_path and "disable_all" not in str_path
 ]
 
 
diff --git a/tests/regrtest_data/fixme.py b/tests/regrtest_data/fixme.py
new file mode 100644
index 0000000000..f0f7d062b2
--- /dev/null
+++ b/tests/regrtest_data/fixme.py
@@ -0,0 +1 @@
+# TODO: implement
diff --git a/tests/test_self.py b/tests/test_self.py
index 3970f22641..83e7421edf 100644
--- a/tests/test_self.py
+++ b/tests/test_self.py
@@ -266,7 +266,7 @@ def test_enable_all_works(self) -> None:
         """
         )
         self._test_output(
-            [module, "--disable=all", "--enable=all", "-rn"], expected_output=expected
+            [module, "--disable=I", "--enable=all", "-rn"], expected_output=expected
         )
 
     def test_wrong_import_position_when_others_disabled(self) -> None: