I'm assuming you are using some sort of cron-job to do Python scraping. You can use the same strategy here: write R script and set it up to run daily at 3 am via cron-job. R already comes with Rscript utility that will run your script. There is also package called littler (you can find more about it here) that does similar stuff.
As for Excel, there is readxl, writexl and openxlsx.
However, I would suggest using some sort of RDBMS (SQLite, for example) to store your data if you don't need Excel files explicitly. If Python saves them and then R reads them, then Excel is not the best data storage solution.