In moderation, yogurt can be a helpful food to eat if you have acid reflux because of its beneficial probiotics and bacteria. Jackson Siegelbaum Gastroenterology in Pennsylvania recommends low-fat or fat-free yogurt.Thick, Greek yogurt with a low percentage of fat can also be used for cooking and in desserts.verview. Acid reflux, heartburn and GERD (gastroesophageal reflux disease) affect millions of people around the world. If you suffer from one of these conditions, your diet most likely plays a huge role in its severity.