Probably PC/104 with an ISA adapter.

These are cute but pricey.

https://www.ebay.com/itm/313599549719

it depends on what qualifies as a motherboard, really

There are tiny processor-on-modules that have ISA but you'd need to build an adapter board or cable - https://www.icop.com.tw/product_list/40

PC104 has adapters already as Plasma stated (shameless plug - Cheap Homebrew ISA->PC104 adapters )

if you want the smallest motherboard with a traditional ISA port then ICOP make some interesting stuff -

You could also use a small ISA backplane with an SBC. If you are not restricted in height that would get you the most slots.

Thanks all! Rasteri, the picture of the MB you inserted in your post looks interesting, but I can't find a link to the supplier's website (ICOP?)
Could you please send that link?

Just a hint: Zida "tomato board" were some really small mainstream boards in, I think, the Socket 3 to slot 1 era.

Choux69 wrote on 2022-05-09, 07:30:

Thanks all! Rasteri, the picture of the MB you inserted in your post looks interesting, but I can't find a link to the supplier's website (ICOP?)
Could you please send that link?

I can't find it on icop's website either but the part number is VDX-6390, should be available from industrial computer suppliers (I can personally reommend DSL in the UK - https://www.dsl-ltd.co.uk/)

EDIT : you can find other vortex86 boards if you check their website - https://www.vortex86.com/products - click on each processor then go to the "EVB" tab to find evaluation boards, that's how I found this one

Plasma wrote on 2022-05-08, 21:27:

Probably PC/104 with an ISA adapter.

Seconded

Hello. Quick follow up: I emailed Vortex to see if the motherboard was still available. There were only 2 left hanging around in their stock but were not functional. No luck but thanks all for your contribution