I have ehlers danlos which isn't even autoimmune and methotrexate has been beneficial for me. It hasn't helped the problems with my larger joints, but it saved me from an additional hand surgery. I was on MTX because when I went off of prednisone my fingers locked up. Because MTX helped me a few years ago, my doctor gave me that per my request and it worked quite well. The only side effect of MTX for me has been GI upset for a day or so, but I wouldn't consider it major GI upset. It wasn't even major enough for me to immediately be able to attribute it to the MTX. I just know that it was after having noticed that it was always the day after taking the dose that I felt not quite as well as I did on the other days.
I have AS and took methotrexate, without side effects, they use it at low dosages. For AS it's usefulness has not been demonstrated, however it is effective for Psoriatic Arthritis. There are many cross over of symptoms between the rheumatic diseases. You can give it a trial. good luck