I want my text font to be Times New Roman 14 and my footnote font Times New Roman 12. The notes are fine, but the footnote numbers are Times New Roman 14. Screen shots:
-john
AMD Ryzen 5 2600 Six-Core Processor, 3.40 GHz, 32.0 GB RAM, Raedon RX 570 Series GPU, 64-bit, Windows 11 Pro, 1TB SSD, 2TB and 4TB HDDs IPad Air (3rd Gen)
Version: 3.1.1.0 (1463331) 64-bit - 03 Nov 2021
Try Preferences>Editing>Formating
That is how it is done in macOS I don’t know about Windows.
Thanks Orpheus for the suggestion but I didn’t see anything that would affect the size of the automatically assigned footnote numbers. I’m stumped.
If you use this to add footnotes :

Meaning that you don’t select any text when adding a footnote, you just have the cursor where you want the footnote’s reference number to be in the text.
And format the resulting footnote marker the same way than the footnote itself,
plus then select the footnote marker and :

I believe this might fix your problem.
What you currently get (or so it seems) is that the footnote number gets the body text attributes rather than the footnote’s. (Whether it makes any sense, or whether it is a bug, being another topic.)
EDIT : I just tried and was unable to reproduce your issue to begin with.
I get this (superscript) :

no matter what.
Thanks Vincent. I am making progress. Endnotes look better than footnotes since the number are superscript and therefore smaller. Will continue to dig into the documentation and see if I can solve it.
-john
Well, this is getting confusing :
Endnotes are nothing else than footnotes gathered at the end of a chapter rather than being at the bottom of the page they relate to. (As a matter of fact, there is no such thing as endnotes anywhere in Scrivener up to when the draft passes through the compiler’s settings.)
I don’t see why they should look any different.
In your compile format, uncheck this :
Pretty sure that will “fix” your issue.
It still doesn’t explain the font size mismatch (I still can’t reproduce the issue), but at least you’ll get superscript in your footnotes. (You said you like it better, so there you go
)