diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8de1820..a6739a3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,12 @@
 # whl2conda changes
 
+## [24.1.1] - *in progress*
+### Features
+* Added persistent user settings for:
+    * default conda format
+    * whether to automatically update stdrenames table
+    * specify aliases for extra pypi indexes
+
 ## [24.4.0] - 2024-4-14
 ### Changes
 * Only use classic installer in `whl2conda install` environments if 
diff --git a/mkdocs.yml b/mkdocs.yml
index bae6165..5d06153 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -30,8 +30,8 @@ theme:
   hljs_languages:
     python
     json
-  logo: whl2conda.svg
-  favicon: whl2conda.svg
+  logo: whl2conda.jpg
+  favicon: whl2conda.jpg
   palette:
     - media: "(prefers-color-scheme: light)"
       scheme: default
diff --git a/src/whl2conda/VERSION b/src/whl2conda/VERSION
index ee3b424..2caa72e 100644
--- a/src/whl2conda/VERSION
+++ b/src/whl2conda/VERSION
@@ -1 +1,2 @@
-24.4.0
+24.4.1
+
diff --git a/src/whl2conda/cli/config.py b/src/whl2conda/cli/config.py
index 309e021..80663a3 100644
--- a/src/whl2conda/cli/config.py
+++ b/src/whl2conda/cli/config.py
@@ -1,4 +1,4 @@
-#  Copyright 2023 Christopher Barber
+#  Copyright 2023-2024 Christopher Barber
 #
 #  Licensed under the Apache License, Version 2.0 (the "License");
 #  you may not use this file except in compliance with the License.
@@ -19,6 +19,7 @@
 from __future__ import annotations
 
 import argparse
+import json
 import sys
 from http.client import HTTPException
 from pathlib import Path
@@ -29,6 +30,7 @@
 from .common import add_markdown_help, dedent
 from ..impl.pyproject import add_pyproject_defaults
 from ..api.stdrename import user_stdrenames_path
+from ..settings import settings
 
 __all__ = ["config_main"]
 
@@ -76,6 +78,26 @@ def config_main(
             %(const)s.
             """),
     )
+
+    settings_opts = parser.add_argument_group("user settings options")
+
+    settings_opts.add_argument(
+        "--remove", metavar="<key>", help="Unset user setting with given key."
+    )
+    settings_opts.add_argument(
+        "--set",
+        metavar=("<key>", "<value>"),
+        nargs=2,
+    )
+
+    settings_opts.add_argument(
+        "--show",
+        metavar="<key>",
+        nargs="?",
+        const="",
+        help=f"Show user settings from {settings._settings_file}",
+    )
+
     parser.add_argument(
         "-n",
         "--dry-run",
@@ -95,6 +117,15 @@ def config_main(
         except Exception as ex:  # pylint: disable=broad-exception-caught
             parser.error(str(ex))
 
+    if parsed.remove:
+        remove_user_setting(parsed.remove)
+
+    if parsed.set:
+        set_user_setting(*parsed.set)
+
+    if parsed.show is not None:
+        show_user_settings(parsed.show)
+
 
 def update_std_renames(renames_file: Path, *, dry_run: bool) -> None:
     """
@@ -124,5 +155,22 @@ def update_std_renames(renames_file: Path, *, dry_run: bool) -> None:
     sys.exit(0)
 
 
+def set_user_setting(key: str, value: str) -> None:
+    settings.set(key, value)
+    settings.save()
+
+
+def show_user_settings(key: str) -> None:
+    if key:
+        print(f"{key}: {json.dumps(settings.get(key))}")
+    else:
+        print(json.dumps(settings.to_dict(), indent=2))
+
+
+def remove_user_setting(key: str) -> None:
+    settings.unset(key)
+    settings.save()
+
+
 if __name__ == "__main__":  # pragma: no cover
     config_main()
diff --git a/src/whl2conda/cli/convert.py b/src/whl2conda/cli/convert.py
index 3c47823..9351df5 100644
--- a/src/whl2conda/cli/convert.py
+++ b/src/whl2conda/cli/convert.py
@@ -31,6 +31,7 @@
 from ..impl.prompt import is_interactive, choose_wheel
 from ..api.converter import Wheel2CondaConverter, CondaPackageFormat, DependencyRename
 from ..impl.pyproject import read_pyproject, PyProjInfo
+from ..settings import settings
 from .common import (
     add_markdown_help,
     dedent,
@@ -452,7 +453,7 @@ def convert_main(args: Optional[Sequence[str]] = None, prog: Optional[str] = Non
     elif pyproj_info.conda_format:
         out_fmt = pyproj_info.conda_format
     else:
-        out_fmt = CondaPackageFormat.V2
+        out_fmt = settings.conda_format
 
     if verbosity < -1:
         level = logging.ERROR
diff --git a/src/whl2conda/cli/main.py b/src/whl2conda/cli/main.py
index c3c7a7f..a2b4ebe 100644
--- a/src/whl2conda/cli/main.py
+++ b/src/whl2conda/cli/main.py
@@ -1,4 +1,4 @@
-#  Copyright 2023 Christopher Barber
+#  Copyright 2023-2024 Christopher Barber
 #
 #  Licensed under the Apache License, Version 2.0 (the "License");
 #  you may not use this file except in compliance with the License.
@@ -20,10 +20,12 @@
 
 import argparse
 import sys
+from pathlib import Path
 from typing import Optional, Sequence
 
 from ..__about__ import __version__
 from .common import dedent, Subcommands, add_markdown_help
+from ..settings import settings
 
 __all__ = ["main"]
 
@@ -83,11 +85,20 @@ def __call__(self, *args, **kwargs):
         "--list-subcommands", action=ListSubcommands, nargs=0, help=argparse.SUPPRESS
     )
 
+    parser.add_argument(
+        "--settings",
+        metavar="<filepath>",
+        help="Override default settings file",
+    )
+
     add_markdown_help(parser)
     parser.add_argument("--version", action="version", version=__version__)
 
     parsed = parser.parse_args(args)
 
+    if parsed.settings:
+        settings.load(Path(parsed.settings).expanduser())
+
     subcmds.run(parsed)
 
 
diff --git a/src/whl2conda/impl/download.py b/src/whl2conda/impl/download.py
index 5819b88..d8e1882 100644
--- a/src/whl2conda/impl/download.py
+++ b/src/whl2conda/impl/download.py
@@ -18,6 +18,7 @@
 
 from __future__ import annotations
 
+import configparser
 import shutil
 import subprocess
 import sys
@@ -25,11 +26,38 @@
 from pathlib import Path
 from typing import Optional
 
+from ..settings import settings
+
 __all__ = [
     "download_wheel",
+    "lookup_pypi_index",
 ]
 
 
+def lookup_pypi_index(index: str) -> str:
+    """
+    Translate index aliases
+
+    First looks for exact match in user settings
+    pyproject_indexes table and then looks for
+    matching entry in the ~/.pypirc file.
+
+    Otherwise returns the original string
+    """
+    if new_index := settings.pypi_indexes.get(index):
+        return new_index
+
+    pypirc_path = Path("~/.pypirc").expanduser()
+    if pypirc_path.exists():
+        pypirc = configparser.ConfigParser()
+        pypirc.read(pypirc_path)
+        try:
+            return pypirc[index]["repository"]
+        except Exception:
+            pass
+    return index
+
+
 def download_wheel(
     spec: str,
     index: str = "",
@@ -61,6 +89,8 @@ def download_wheel(
             "--implementation",
             "py",
         ]
+        if index:
+            index = lookup_pypi_index(index)
         if index:
             cmd.extend(["-i", index])
         cmd.extend(["-d", str(tmpdirname)])
diff --git a/src/whl2conda/impl/pyproject.py b/src/whl2conda/impl/pyproject.py
index 60a8b58..f9fdcc6 100644
--- a/src/whl2conda/impl/pyproject.py
+++ b/src/whl2conda/impl/pyproject.py
@@ -34,7 +34,7 @@
 ]
 
 
-class CondaPackageFormat(enum.Enum):
+class CondaPackageFormat(str, enum.Enum):
     """
     Supported output package formats
 
diff --git a/src/whl2conda/settings.py b/src/whl2conda/settings.py
new file mode 100644
index 0000000..71e4ced
--- /dev/null
+++ b/src/whl2conda/settings.py
@@ -0,0 +1,241 @@
+#  Copyright 2024 Christopher Barber
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+#
+"""
+Settings for whl2conda.
+"""
+
+from __future__ import annotations
+
+# standard
+import dataclasses
+import datetime as dt
+import json
+from pathlib import Path
+from typing import Any, Callable, ClassVar, NamedTuple, Union
+
+# third party
+from platformdirs import user_config_path
+
+# this project
+from .__about__ import __version__
+from .impl.pyproject import CondaPackageFormat
+
+__all__ = ["Whl2CondaSettings", "settings"]
+
+
+class FieldDefault(NamedTuple):
+    factory: Callable
+
+
+class StringConversionField:
+    def __init__(self, *, default):
+        if callable(default):
+            self._default = FieldDefault(default)
+        else:
+            self._default = default
+
+    def __set_name__(self, owner, name):
+        self._name = "_" + name
+
+    def __get__(self, obj, type):
+        if obj is None:
+            return self._default
+        return getattr(obj, self._name)
+
+    def __set__(self, obj, value):
+        if isinstance(value, FieldDefault):
+            value = value.factory()
+        elif isinstance(value, str):
+            value = self._convert_from_str(value)
+        setattr(obj, self._name, value)
+
+    def __delete__(self, obj):
+        self.__set__(obj, self._default)
+
+    def _convert_from_str(self, value: str):
+        return value
+
+
+class BoolField(StringConversionField):
+    def __init__(self, *, default: bool = False):
+        super().__init__(default=default)
+
+    def _convert_from_str(self, value: str):
+        value = value.lower()
+        if value in {"true", "t", "yes", "y"}:
+            return True
+        elif value in {"false", "f", "no", "n"}:
+            return False
+        else:
+            raise ValueError(f"Invalid value {value!r} for bool field")
+
+
+class CondaPackageFormatField(StringConversionField):
+    def __init__(self):
+        super().__init__(default=CondaPackageFormat.V2)
+
+    def _convert_from_str(self, value: str):
+        return CondaPackageFormat.from_string(value)
+
+
+def toidentifier(name: str) -> str:
+    return name.replace("-", "_")
+
+
+def fromidentifier(name: str) -> str:
+    return name.replace("_", "-")
+
+
+@dataclasses.dataclass(kw_only=True)
+class Whl2CondaSettings:
+    SETTINGS_FILENAME: ClassVar[str] = "whl2conda.json"
+    DEFAULT_SETTINGS_FILE: ClassVar[Path] = user_config_path() / SETTINGS_FILENAME
+
+    # TODO:
+    #   - difftool
+    #   - pyproject defaults
+
+    auto_update_std_renames: BoolField = BoolField()
+
+    conda_format: CondaPackageFormatField = CondaPackageFormatField()
+
+    pypi_indexes: StringConversionField = StringConversionField(default=dict)
+
+    #
+    # Internal attributes
+    #
+
+    _settings_file: Path = dataclasses.field(
+        default=DEFAULT_SETTINGS_FILE, compare=False
+    )
+
+    _fieldnames: ClassVar[frozenset[str]] = frozenset()
+
+    @property
+    def settings_file(self) -> Path:
+        """
+        Settings file for this settings object.
+
+        Set from [from_file][..] constructor or else will be
+        [DEFAULT_SETTINGS_FILE][(c).].
+        """
+        return self._settings_file
+
+    def to_dict(self) -> dict[str, Any]:
+        return {
+            k: v for k, v in dataclasses.asdict(self).items() if not k.startswith("_")
+        }
+
+    def get(self, key: str) -> Any:
+        name, subkey = self._split_key(key)
+        value = getattr(self, name)
+
+        if subkey:
+            if not isinstance(value, dict):
+                raise KeyError(
+                    f"Bad settings key '{key}': '{name}' is not a dictionary"
+                )
+            if subkey not in value:
+                raise KeyError(f"'{key}' is not set'")
+            value = value[subkey]
+
+        return value
+
+    def set(self, key: str, value: Any) -> None:
+        name, subkey = self._split_key(key)
+
+        if not subkey:
+            setattr(self, name, value)
+
+        else:
+            d = getattr(self, name)
+            if not isinstance(d, dict):
+                raise KeyError(
+                    f"Bad settings key '{key}': '{name}' is not a dictionary"
+                )
+            d[subkey] = value
+
+    def unset(self, key: str) -> None:
+        """
+        Unset attribute with given key.
+
+        The setting will revert to its original value.
+        """
+        name, subkey = self._split_key(key)
+
+        if not subkey:
+            delattr(self, name)
+
+        else:
+            d = getattr(self, name)
+            if not isinstance(d, dict):
+                raise KeyError(
+                    f"Bad settings key '{key}': '{name}' is not a dictionary"
+                )
+            try:
+                del d[subkey]
+            except KeyError:
+                pass
+
+    def _split_key(self, key: str) -> tuple[str, str]:
+        parts = key.split(".", maxsplit=1)
+        name = toidentifier(parts[0])
+        if name not in self._fieldnames:
+            raise KeyError(f"Unknown settings key '{key}'")
+        return name, parts[1] if len(parts) > 1 else ""
+
+    @classmethod
+    def from_file(cls, filename: Union[Path, str] = "") -> Whl2CondaSettings:
+        settings = cls()
+        settings.load(filename or cls.DEFAULT_SETTINGS_FILE)
+        return settings
+
+    def load(self, filename: Union[Path, str], reset_all: bool = False) -> None:
+        filepath = Path(Path(filename).expanduser())
+        self._settings_file = filepath
+        if reset_all:
+            self.unset_all()
+        if filepath.exists():
+            contents = filepath.read_text("utf8")
+            json_obj = json.loads(contents)
+            for k, v in json_obj.items():
+                if k in self._fieldnames:
+                    setattr(self, k, v)
+
+    def save(self, filename: Union[Path, str] = "") -> None:
+        """
+        Write settings to specified file in JSON format.
+        Args:
+            filename: file to write. Defaults to [settings_file][..]
+        """
+        filepath = Path(filename or self._settings_file)
+        json_obj = self.to_dict()
+        json_obj["$whl2conda-version"] = __version__
+        json_obj["$created"] = str(dt.datetime.now())
+        filepath.write_text(json.dumps(json_obj, indent=2))
+
+    def unset_all(self) -> None:
+        """
+        Unset all settings, and revert to default values.
+        """
+        for k in self._fieldnames:
+            self.unset(k)
+
+
+Whl2CondaSettings._fieldnames = frozenset(
+    f.name for f in dataclasses.fields(Whl2CondaSettings) if not f.name.startswith("_")
+)
+
+settings = Whl2CondaSettings.from_file()
diff --git a/test/conftest.py b/test/conftest.py
index 2162b63..85baae1 100644
--- a/test/conftest.py
+++ b/test/conftest.py
@@ -1,4 +1,4 @@
-#  Copyright 2023 Christopher Barber
+#  Copyright 2023-2024 Christopher Barber
 #
 #  Licensed under the Apache License, Version 2.0 (the "License");
 #  you may not use this file except in compliance with the License.
@@ -23,6 +23,16 @@
 
 import pytest
 
+from whl2conda.settings import settings
+
+
+@pytest.fixture(autouse=True)
+def clear_settings():
+    """
+    Fixture clears user settings before each test
+    """
+    settings.unset_all()
+
 
 def pytest_addoption(parser):
     """
diff --git a/test/test_settings.py b/test/test_settings.py
new file mode 100644
index 0000000..7067f93
--- /dev/null
+++ b/test/test_settings.py
@@ -0,0 +1,165 @@
+#  Copyright 2024 Christopher Barber
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+#
+"""
+Unit tests for whl2conda.settings module
+"""
+
+import tempfile
+from pathlib import Path
+from typing import Any
+
+import pytest
+
+from whl2conda.impl.pyproject import CondaPackageFormat
+from whl2conda.settings import Whl2CondaSettings, fromidentifier
+
+# ruff: noqa: F811
+
+
+def test_Whl2CondaSettings(tmp_path: Path):
+    """
+    Unit test for Whl2CondaSettings class
+    """
+
+    settings = Whl2CondaSettings()
+
+    # check defaults
+    assert settings.settings_file
+    assert settings.auto_update_std_renames is False
+    assert settings.conda_format is CondaPackageFormat.V2
+    assert settings.pypi_indexes == {}
+
+    check_settings(settings, tmp_path)
+
+    settings.auto_update_std_renames = True
+    assert settings.auto_update_std_renames is True
+    settings.auto_update_std_renames = "Yes"
+    assert settings.auto_update_std_renames is True
+    with pytest.raises(ValueError):
+        settings.auto_update_std_renames = "bogus"
+
+    settings.conda_format = "V1"
+    assert settings.conda_format is CondaPackageFormat.V1
+
+    settings.pypi_indexes["somewhere"] = "https://somewhere.com/pypi"
+    assert settings.pypi_indexes == {"somewhere": "https://somewhere.com/pypi"}
+    check_settings(settings, tmp_path)
+
+
+def test_settings_get() -> None:
+    """Unit test for Whl2CondaSettings.get method"""
+    settings = Whl2CondaSettings()
+
+    settings.auto_update_std_renames = True
+    assert settings.get("auto-update-std-renames") is True
+
+    with pytest.raises(KeyError, match=r"Unknown settings key 'barf'"):
+        settings.get("barf")
+
+    assert settings.get("pypi_indexes") is settings.pypi_indexes
+
+    with pytest.raises(KeyError, match="'pypi-indexes.somewhere' is not set"):
+        settings.get("pypi-indexes.somewhere")
+
+    with pytest.raises(KeyError, match="Bad settings key 'conda_format.value'"):
+        settings.get("conda_format.value")
+
+    settings.pypi_indexes["somewhere"] = "https://somewhere.com/pypi"
+    assert settings.get("pypi_indexes.somewhere") == "https://somewhere.com/pypi"
+
+
+def test_settings_set(tmp_path: Path) -> None:
+    """Unit test for Whl2CondaSettings.set method"""
+    settings = Whl2CondaSettings()
+
+    settings.set("auto-update-std-renames", True)
+    assert settings.auto_update_std_renames is True
+
+    settings.set("auto-update-std-renames", "no")
+    assert settings.auto_update_std_renames is False
+
+    settings.set("pypi-indexes.somewhere", "https://somewhere.com/pypi")
+    assert settings.pypi_indexes == {"somewhere": "https://somewhere.com/pypi"}
+
+    settings.set("pypi-indexes.somewhere-else", "https://other.com/pypi")
+    assert settings.pypi_indexes == {
+        "somewhere": "https://somewhere.com/pypi",
+        "somewhere-else": "https://other.com/pypi",
+    }
+
+    settings.set("pypi-indexes.somewhere", "https://whoops")
+    assert settings.pypi_indexes == {
+        "somewhere": "https://whoops",
+        "somewhere-else": "https://other.com/pypi",
+    }
+
+    with pytest.raises(KeyError, match="'conda_format' is not a dictionary"):
+        settings.set("conda_format.value", "V2")
+
+    check_settings(settings, tmp_path)
+
+
+def test_settings_unset(tmp_path: Path) -> None:
+    """
+    Unit test for Whl2CondaSettings.unset method
+    """
+    settings = Whl2CondaSettings()
+
+    settings.conda_format = "V1"
+    assert settings.conda_format is CondaPackageFormat.V1
+
+    settings.pypi_indexes["somewhere"] = "https://somewhere.com/pypi"
+    settings.pypi_indexes["nowhere"] = "https://nowhere.com/pypi"
+
+    settings.unset("pypi-indexes.somewhere")
+    assert settings.pypi_indexes == {"nowhere": "https://nowhere.com/pypi"}
+
+    settings.unset("pypi-indexes")
+    assert settings.pypi_indexes == {}
+
+    settings.unset("conda_format")
+    assert settings.conda_format is CondaPackageFormat.V2
+
+    # no error
+    settings.unset("pypi-indexes.notset")
+
+    with pytest.raises(KeyError, match="'conda_format' is not a dictionary"):
+        settings.unset("conda_format.value")
+
+
+def check_settings(settings: Whl2CondaSettings, tmp_path: Path) -> None:
+    """
+    Check invariants on Whl2CondaSettings instance
+    """
+    fname = tempfile.mktemp(prefix="whl2conda", suffix=".json", dir=tmp_path)
+    settings.save(fname)
+    settings2 = Whl2CondaSettings.from_file(fname)
+    assert settings2.settings_file == Path(fname)
+    assert settings == settings2
+
+    for name in Whl2CondaSettings._fieldnames:
+        assert settings.get(fromidentifier(name)) == getattr(settings, name)
+
+    settings_dict = settings.to_dict()
+
+    def _check_dict(d: dict[str, Any], prefix="") -> None:
+        for k, v in d.items():
+            key = f"{prefix}{k}"
+            if isinstance(v, dict):
+                _check_dict(v, prefix=key + ".")
+            else:
+                assert settings.get(key) == v
+
+    _check_dict(settings_dict)