diff --git a/README.md b/README.md
index dcb6321c4..6d9f01b68 100644
--- a/README.md
+++ b/README.md
@@ -290,18 +290,26 @@ for a `.pip-tools.toml` file and then in your `pyproject.toml`. You can
 also specify an alternate TOML configuration file with the `--config` option.
 
 For example, to by default generate `pip` hashes in the resulting
-requirements file output, you can specify in a configuration file
+requirements file output, you can specify in a configuration file:
 
 ```toml
 [tool.pip-tools]
 generate-hashes = true
-
 ```
 
 Options to `pip-compile` and `pip-sync` that may be used more than once
 must be defined as lists in a configuration file, even if they only have one
 value.
 
+`pip-tools` supports default values vor [all valid command-line flags](/cli/index.md)
+of its subcommands. Configuration keys may contain underscores instead of dashes,
+so the above could also be specified in this format:
+
+```toml
+[tool.pip-tools]
+generate_hashes = true
+```
+
 You might be wrapping the `pip-compile` command in another script. To avoid
 confusing consumers of your custom script you can override the update command
 generated at the top of requirements files by setting the
diff --git a/piptools/utils.py b/piptools/utils.py
index 68a46f51d..de2418473 100644
--- a/piptools/utils.py
+++ b/piptools/utils.py
@@ -58,6 +58,9 @@
     "--no-config",
 }
 
+# Set of option that are only negative, i.e. --no-<option>
+ONLY_NEGATIVE_OPTIONS = {"--no-index"}
+
 
 def key_from_ireq(ireq: InstallRequirement) -> str:
     """Get a standardized key for an InstallRequirement."""
@@ -560,7 +563,7 @@ def override_defaults_from_config_file(
     else:
         config_file = Path(value)
 
-    config = parse_config_file(config_file)
+    config = parse_config_file(ctx, config_file)
     if config:
         _validate_config(ctx, config)
         _assign_config_to_cli_context(ctx, config)
@@ -659,17 +662,6 @@ def select_config_file(src_files: tuple[str, ...]) -> Path | None:
 }
 
 
-def get_click_dest_for_option(option_name: str) -> str:
-    """
-    Returns the click ``dest`` value for the given option name.
-    """
-    # Format the keys properly
-    option_name = option_name.lstrip("-").replace("-", "_").lower()
-    # Some options have dest values that are overrides from the click generated default
-    option_name = NON_STANDARD_OPTION_DEST_MAP.get(option_name, option_name)
-    return option_name
-
-
 # Ensure that any default overrides for these click options are lists, supporting multiple values
 MULTIPLE_VALUE_OPTIONS = [
     "extras",
@@ -681,7 +673,19 @@ def get_click_dest_for_option(option_name: str) -> str:
 ]
 
 
-def parse_config_file(config_file: Path) -> dict[str, Any]:
+def get_cli_options(ctx: click.Context) -> dict[str, click.Parameter]:
+    cli_opts = {
+        opt: option
+        for option in ctx.command.params
+        for opt in itertools.chain(option.opts, option.secondary_opts)
+        if opt.startswith("--") and option.name is not None
+    }
+    return cli_opts
+
+
+def parse_config_file(
+    click_context: click.Context, config_file: Path
+) -> dict[str, Any]:
     try:
         config = tomllib.loads(config_file.read_text(encoding="utf-8"))
     except OSError as os_err:
@@ -697,9 +701,13 @@ def parse_config_file(config_file: Path) -> dict[str, Any]:
 
     # In a TOML file, we expect the config to be under `[tool.pip-tools]`
     piptools_config: dict[str, Any] = config.get("tool", {}).get("pip-tools", {})
-    piptools_config = {
-        get_click_dest_for_option(k): v for k, v in piptools_config.items()
-    }
+
+    piptools_config = _normalize_keys_in_config(piptools_config)
+    piptools_config = _invert_negative_bool_options_in_config(
+        ctx=click_context,
+        config=piptools_config,
+    )
+
     # Any option with multiple values needs to be a list in the pyproject.toml
     for mv_option in MULTIPLE_VALUE_OPTIONS:
         if not isinstance(piptools_config.get(mv_option), (list, type(None))):
@@ -710,6 +718,45 @@ def parse_config_file(config_file: Path) -> dict[str, Any]:
     return piptools_config
 
 
+def _normalize_keys_in_config(config: dict[str, Any]) -> dict[str, Any]:
+    return {_normalize_config_key(key): value for key, value in config.items()}
+
+
+def _invert_negative_bool_options_in_config(
+    ctx: click.Context, config: dict[str, Any]
+) -> dict[str, Any]:
+    new_config = {}
+    cli_opts = get_cli_options(ctx)
+
+    for key, value in config.items():
+        # Transform config key to its equivalent in the CLI
+        long_option = _convert_to_long_option(key)
+        new_key = cli_opts[long_option].name if long_option in cli_opts else key
+        assert new_key is not None
+
+        # Invert negative boolean according to the CLI
+        new_value = (
+            not value
+            if long_option.startswith("--no-")
+            and long_option not in ONLY_NEGATIVE_OPTIONS
+            and isinstance(value, bool)
+            else value
+        )
+        new_config[new_key] = new_value
+
+    return new_config
+
+
+def _normalize_config_key(key: str) -> str:
+    """Transform given ``some-key`` into ``some_key``."""
+    return key.lstrip("-").replace("-", "_").lower()
+
+
+def _convert_to_long_option(key: str) -> str:
+    """Transform given ``some-key`` into ``--some-key``."""
+    return "--" + key.lstrip("-").replace("_", "-").lower()
+
+
 def is_path_relative_to(path1: Path, path2: Path) -> bool:
     """Return True if ``path1`` is relative to ``path2``."""
     # TODO: remove this function in favor of Path.is_relative_to()
diff --git a/tests/test_cli_compile.py b/tests/test_cli_compile.py
index 693054400..90267ea6a 100644
--- a/tests/test_cli_compile.py
+++ b/tests/test_cli_compile.py
@@ -3017,3 +3017,40 @@ def test_raise_error_on_invalid_config_option(
 
     assert out.exit_code == 2
     assert "Invalid value for config key 'dry_run': ['invalid', 'value']" in out.stderr
+
+
+def test_cli_boolean_flag_config_option_has_valid_context(
+    pip_conf, runner, tmp_path, make_config_file
+):
+    config_file = make_config_file("no-annotate", True)
+
+    req_in = tmp_path / "requirements.in"
+    req_in.write_text("small-fake-a==0.1")
+    out = runner.invoke(
+        cli,
+        [
+            req_in.as_posix(),
+            "--config",
+            config_file.as_posix(),
+            "--no-emit-options",
+            "--no-header",
+            "--output-file",
+            "-",
+        ],
+    )
+    assert out.exit_code == 0
+    assert out.stdout == "small-fake-a==0.1\n"
+
+
+def test_invalid_cli_boolean_flag_config_option_captured(
+    pip_conf, runner, tmp_path, make_config_file
+):
+    config_file = make_config_file("no-annnotate", True)
+
+    req_in = tmp_path / "requirements.in"
+    req_in.touch()
+
+    out = runner.invoke(cli, [req_in.as_posix(), "--config", config_file.as_posix()])
+
+    assert out.exit_code == 2
+    assert "No such config key 'no_annnotate'." in out.stderr
diff --git a/tests/test_utils.py b/tests/test_utils.py
index f06a42100..76ea0d612 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -20,7 +20,7 @@
     flat_map,
     format_requirement,
     format_specifier,
-    get_click_dest_for_option,
+    get_cli_options,
     get_compile_command,
     get_hashes_from_ireq,
     get_pip_version_for_python_executable,
@@ -585,7 +585,7 @@ def test_get_sys_path_for_python_executable():
         ("pip-args", "changed"),
         ("pre", True),
         ("rebuild", True),
-        ("extras", ["changed"]),
+        ("extra", ["changed"]),
         ("all-extras", True),
         ("index-url", "changed"),
         ("header", False),
@@ -615,10 +615,11 @@ def test_callback_config_file_defaults(pyproject_param, new_default, make_config
     # Create a "compile" run example pointing to the config file
     ctx = Context(compile_cli)
     ctx.params["src_files"] = (str(config_file),)
+    cli_opts = get_cli_options(ctx)
     found_config_file = override_defaults_from_config_file(ctx, "config", None)
     assert found_config_file == config_file
     # Make sure the default has been updated
-    lookup_param = get_click_dest_for_option(pyproject_param)
+    lookup_param = cli_opts["--" + pyproject_param].name
     assert ctx.default_map[lookup_param] == new_default
 
 
@@ -661,8 +662,7 @@ def test_callback_config_file_defaults_precedence(make_config_file):
     found_config_file = override_defaults_from_config_file(ctx, "config", None)
     # The pip-tools specific config file should take precedence over pyproject.toml
     assert found_config_file == piptools_config_file
-    lookup_param = get_click_dest_for_option("newline")
-    assert ctx.default_map[lookup_param] == "LF"
+    assert ctx.default_map["newline"] == "LF"
 
 
 def test_callback_config_file_defaults_unreadable_toml(make_config_file):
diff --git a/tox.ini b/tox.ini
index 01ab8716d..fcf3a6bfc 100644
--- a/tox.ini
+++ b/tox.ini
@@ -112,7 +112,7 @@ commands =
     -W \
     -d "{temp_dir}/.doctrees" \
     . \
-    --watch ../README.rst \
+    --watch ../README.md \
     --watch ../CHANGELOG.md \
     "{envdir}/docs_out"