I want to enable infinite scrolling on my category pages rather than a paginated view. However I am concerned this may affect Google indexing.

I.e. if the products are loaded as the user scrolls, is the google indexer going to be able to follow these links as they wont be on the page on the initial load.

If you search google for "infinite scroll seo" you can see lots of articles warning against using infinite scroll unless there is a way on the page to also load the product links.