Though they’ve gotten a bad reputation for causing uncomfortable side effects, beans are actually one of the healthiest foods you can eat. The USDA’s Food Guide Pyramid includes beans on two lists: protein sources and vegetables. They’re full of non-fat protein, “good” complex carbohydrates and fiber. It’s mostly the fiber that causes problems, especially if your system is not used to it and you add a lot of beans to your diet all at once.
Cramping
Fiber is the component of beans that the body cannot digest. Fiber moves straight through your system, and this is healthy. But if you overdo quantities, fiber can temporarily slow down your bowels, because it is indigestible. This can result in painful cramping.
Flatulence
Beans are notorious for causing flatulence. It happens when the bacteria in your intestines react to their fiber content. The good news is that lentils may be less likely to have this effect than other beans. Experiment to find out which kind of beans, if any, cause a less significant reaction in your body.
Diarrhea or Constipation
Fiber helps prevent constipation by moving food through your intestines. Too many beans can take a good thing a little bit too far, however, and sometimes diarrhea can result. The flip side to this is that if you don’t drink enough liquids, beans can actually constipate you. They’re high in both insoluble and soluble fiber, and soluble fiber needs liquid to move through your system as it should.
Weight Gain
Though beans contain complex carbohydrates as opposed to simple carbohydrates, 1 cup fills 15 percent of your daily needs. If you eat other carbs during other meals, and you do this routinely, you might find yourself gaining weight. Beans are also relatively high in calories. A cup of baked beans cooked in tomato sauce -- not even molasses or sweet sauce -- can contain up to 250 calories.
Recommendations
Water is the key to most bean side effects. Boiling beans softens their fiber content, and drinking plenty of fluids helps them move through your digestive tract more efficiently, eliminating problems with flatulence, cramping and constipation. Eating them in moderation is also important. AmericanBean.org recommends keeping your consumption to about 1/2 cup per day. You should also increase to that amount gradually, not all at once, if beans have not been a regular part of your diet.
Source: https://www.livestrong.com/article/404674-the-side-effects-of-beans/