This idiom comes from having to take pills as medicine. Many times pills are pretty awful tasting, no? So when you have to do something difficult in order to get better in life, we say that the difficult thing was a bitter pill to swallow. See how that works? It is an unpleasant fact that has to be accepted. It does not involve pills or swallowing. Here is an example, it was a bitter pill for her brother to swallow when she married his enemy. Or, we found his deception a bitter pill to swallow.
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