Yes, a baby can be in a diaper while doing pūjā.

From a Jain point of view:

• The main thing in pūjā is bhāv (inner feeling) – respect, love for Tīrthankars, and pure intention.
• A small child has very innocent, śuddha bhāv. Their clothes or diaper do not make their soul impure.
• For babies, hygiene and safety are most important. A clean diaper is better than the baby being uncomfortable or unclean.
• Parents should just make sure:

- The baby is reasonably clean (wiped, in a fresh diaper). - No disrespect is done knowingly (no shoes on the asan, no playing roughly with idols, etc.). - Any actual soiling (pee/poop leaking, bad smell) near the altar is cleaned quickly and calmly.

In Digambar and Shvetāmbara traditions there is more strictness for adult dress and shuddhi, but such rules are not applied to infants in the same way. For them it is more like simple saṁskār / habit building, not formal ritual.

So yes, you may lovingly let your baby sit or “do pūjā” in a diaper, keeping cleanliness and respect in mind.