Should I under-cook vegetables if I plan on microwaving them the next day? I usually make chicken and stir fry veg for my lunch the following day. Obviously I cook the chicken fully but I was wondering if I plan on only eating the meal the following day and heating it in the microwave for 2 mins @ 1000w, should I under-cook the vegetables a little bit?

The vegetables are usually onions, peppers and spinach.
The vegetables are likely to cook more during the reheating process, so if you don't want that you'll have to cook them less initially. They won't be the same as if you'd stir-fried them to perfection and eaten them straight away of course, but this is something I do myself when preparing meals to reheat at work.

So, basically, the answer to your question is "yes".