After being diagnosed with a bacterial infection, I was prescribed amoxicillin. I am 4 days into the course in which I take 2 625mg tablets per day. Amoxicillin side effects. Amoxicillin is a penicillin antibiotic used to treat bacterial infections, including bronchitis, pneumonia, and infections of the ear, nose, throat, skin, and urinary tract. Bill, Black stools are an indication of blood that has oxidized in your stool. It is not caused by either antibiotics. It can be caused by taking iron supplements and Pepto Bismol. Helpful, trusted answers from doctors: Dr. Fowler on can antibiotics change the color of your stool: About one third of the solid matter in stool is dead bacteria. Also, the actions of bacteria on bilirubin influences the color of stool. We have trillions of bacteria in our intestines and antibiotics kill many of these bacteria, influencing the color of our stool. I advise taking probiotic. Common Questions and Answers about Amoxicillin side effects black stool amoxil I was reading about numbness and tingling in hands and feet and you make several references to long term side effects from quinolones. Welcome to the gastroenterology community! Antibiotics often have diarrhea as a side effect, or this could be something like C Diff. However the black stool is concerning and this would make me think this is more likely to be C Diff. You should remember that some anti-diarrheal drugs can also interfere with the color of your poop, sometimes making them yellow or black. Advertisement When diarrhea stops, your stools should return to their normal color. Ive been taking amoxicillin and flagyl,now my stool is black, is yhis normal? - Answered by a verified Doctor. We use cookies to give you the best possible experience on our website. By continuing to use this site you consent to the use of cookies on your device as described in our cookie policy unless you have disabled them. Medical. Have medical questions? Ask a doctor online! Ask a Doctor. Applies to amoxicillin: oral capsule, oral powder for reconstitution, oral tablet, oral tablet chewable, oral tablet dispersible, oral tablet extended release General The most frequently reported side effects were diarrhea, nausea, and skin rash. Your stool can tell you plenty about what’s going on inside the body, give you a thumbs up regarding your intestinal well-being, or flag a cause for concern.