Sync footnote body and reference number in InDesign

A client recently asked me to make the footnotes numbers in both the body text and in the reference to look the same. Since the footnote in the body is superscript, they wanted the reference number to also be superscript. There isn't necessarily an automatic way to make this happen in the footnote panel, and the reference number usually goes with the paragraph style designated for footnotes. Here's how I made this happen.

So as you can see here, the footnote reference is not superscripted, and followed the same style as the rest of the footnote. This is the standard way InDesign creates this number. 

Make a "footnote style" character style, and a "footnote style" paragraph style. The paragraph style should contain the formatting you want for the footnote body. The only thing you should do with the character style here is make sure that it's superscript (or any difference you want from the reference number and the footnote text). As with all character styles, it should exist only as an exception to the paragraph style. Because my client wanted the footnote numbers in the body and the reference to match, I added in the font, formatting, and size. 

In the footnote panel, apply the character style you made as the character style, and the paragraph style you made as the paragraph style. Even after doing this, however, you'll notice no change in the footnote reference number. To make that work, I added the "footnote style" character style to the paragraph style as a nested style. 

By adding the character style to the paragraph style via nested styles, the first word (in this case) will show up as the character style, which is however your footnote number in the body looks like. I find this to be a good solution, since the footnote body and reference numbers are now linked by formatting, so changing the footnote character style will update both.