Crohn's (active disease) doesn't lower your immune system.
But most (all? open question) people with crohn have a weakened immune response.
Reason for this is genetics, NOD2 and ATG16L1 are often mutated (slightly defective if you will) in people with crohn.
NOD2 and ATG16L1 are both directly involved in autophagy, autophagy is crucial to stop infections. NOD2 is able to recognise bacteria, and it recruits ATG16L1 protein to the site of infection, NOD2 can down or upregulate the defense mechanism of autophagy.
The test to show this is what happens in people with CD have been many, because it's an easy test. You take a harmless pathogen, you inject it in a person with crohn and you do the same thing in a healthy person, you check the blood and see who clears the bacteria fastest, the person with crohn will be slower.