Note: There is another issue Text instead of logo in the template header, but the solution there didn't solve my problem.
I installed mkdocs and mkdocs-material both through pip. The official docs are suggesting me to create a new file my-site/partials/header.html and make the required changes, but it didn't work for me. There are two ways to install the theme, either through pip or by cloning the theme repo. I think the overriding partials method explained in the user-guide is applicable when we actually clone the repo, or am I missing something?
And @squidfunk, Thank you so much for the awesome work!
Hi,
I have Material installed through pip and overriding partials is working fine for me.
Maybe show us your folder structure and configuration file.
Thank You @makshh for the response!
Following was my folder structure when I tried to override the default header.

https://squidfunk.github.io/mkdocs-material/customization/#setup-and-theme-structure
Reference the Material theme as usual in your mkdocs.yml, and create a _new folder_ for overrides, e.g. theme, which you reference using _custom_dir_.
https://squidfunk.github.io/mkdocs-material/customization/#overriding-partials
In order to override the footer, we can replace the footer.html partial with our own partial. To do this, create the file partials/footer.html in the _theme_ directory. MkDocs will now use the new partial when rendering the theme. This can be done with any file.
theme) inside your project (on the same level as assets folder).custom_dir: 'theme' in theme options in your configuration file.Thank You @makshh , the custom_dir setting in the mkdocs.yml worked for me.
Closing this as solved. Thanks @makshh for answering this one!
Most helpful comment
https://squidfunk.github.io/mkdocs-material/customization/#setup-and-theme-structure
https://squidfunk.github.io/mkdocs-material/customization/#overriding-partials
theme) inside your project (on the same level as assets folder).custom_dir: 'theme'in theme options in your configuration file.