@amitydigital said in WordPress Sub-directory for SEO:
Google will view it as one site so you shouldn't have any issues from that perspective. The Google bot is just looking at pages and won't know/care that the underlying CMS that is running some pages is a different install than other pages. The downside is you now have two websites to maintain, two themes, two sets of files, etc... That may result in a bit of a headache in the future.
As @amitydigital put it, the issue with your approach would be repetitive tasks. You will not loose any DA nor PA (being that you implement a correct 301 redirection). What is going to be on the subdirectory?