Taking anxiety meds with chron’s

I was recently prescribed 50mg of Zoloft for anxiety and since starting it (I’m on day 3) I have had AWFUL diarrhea and upset stomach. I was super excited to start it to hopefully help my anxiety, but now I’m worried this could put me back into a flare. Has anyone has this experience with SSRI medications? Will it get better? I am finally back in remission after an almost 2 year long flare and I’m terrified I’m going to mess it up again.