That's the result of a balance between different microbes and their own defensive measures. Entirely novel microbes and biological functions could overwhelm all of that. Hell, if they have just evolved a next level ATP, they could have access to an order of magnitude more energy than our microbes and bodies can use, in which case we'd probably have no chance unless it doesn't recognize us as food.

It's not guaranteed to happen, but with 0 data about alternate evolution trees, any reasoning about the odds is speculation (including my use of "decent chance").

Edit: This would be the case for viruses. Unless they work very differently or our biochemistry has some convergent evolutions, alien viruses should be harmless to us and vice versa. Just like the hundreds of viruses we are exposed to with every breath, most don't react to our cells any differently from how they'd react to wet rocks.