I had to write a plug-in to be able to get it to support multiple sites:
https://github.com/sumdog/jekyll-multisite/
(I'm working on getting tests setup in containers so I can support multiple Jekyll versions and accept pull requests).
If you're starting from scratch, I'm not sure if I'd suggest Jekyll today. I mean it still works for me, but the path has been frustrating and I've found a lot of limitations with it. I wrote a lot of custom ruby plugins to get what I wanted out of it.
I've used Middleman on another project, which was decent, but at the time it lacks some of the more complicated templating Jekyll has. It may have improved since then.
I briefly looked at Hugo. It looks interesting and is worth checking out as well.