Munich to Amsterdam - night train or flight?

I haven't taken that exact route, but the night train is a good choice. It saves you one night in a hotel. And you can go to bed in the evening in Germany and wake up the next day in the Netherlands without having to go through the hassle of security checks an airport faff. And without having to spend 1.5 hours in a tiny seat. And after a breakfast onboard you arrive right in central Amsterdam.

How well do you sleep? Will you sleep through 5 stops between Munich and Amsterdam? I know that I would be good for nothing the next day. Personally, I'd fly every time for this distance, but that's just me.

Something like 12 hours is a consideration, but the departure and arrival times are pretty good. The difference in carbon footprint sort of makes it the right thing to do; and you save on the cost of a hotel room for the night so overall its hundreds of dollars cheaper. And, if you have never done a night train before, well, you gotta do it once in your life.

I also think it depends what you are planning.

I've rode on a night train in the US and even with a bunk, I slept about 2 hours total. Swaying, stops and horns all woke me up.

I would honestly fly but some people can sleep soundly so YVMV.

Horns won't be a problem between Munich and Amsterdam.