If I disabled Prettier as the default formatter, it would not format on save anymore, but my Python would be formatted by autopep8 on save. With this in mind, the following solution worked for me to have both Prettier working for other languages and autopep8 for Python:

{
  "workbench.iconTheme": "vscode-icons",
  "workbench.editorAssociations": [
    {
      "viewType": "jupyter.notebook.ipynb",
      "filenamePattern": "*.ipynb"
    }
  ],
  "git.confirmSync": false,
  "editor.formatOnPaste": true,
  "editor.formatOnSave": true,
  "python.formatting.provider": "autopep8",
  "explorer.confirmDelete": false,
  "python.showStartPage": false,
  "explorer.confirmDragAndDrop": false,
  "python.linting.pylintArgs": ["--load-plugins=pylint_django"],
  "javascript.updateImportsOnFileMove.enabled": "always",
  "editor.defaultFormatter": "esbenp.prettier-vscode",
  "[python]": {
    "editor.defaultFormatter": "ms-python.python"
  }
}

Let me know if somebody finds a better solution!