Through targeted sentence cards.
Various methods of isolated kanji study usually don't cover kanji readings. If they do, they have you learn the most common reading, as KanjiDamage does, for example. Knowing the most common reading helps a little, but you still need to learn how to read actual words you come across by yourself.
After you're done with isolated kanji study, learn kanji readings in context. Readings should not be learned in isolation. You're going to learn words and their readings at the same time. So what you need to do is read a lot of native Japanese content, look up words and make TSCs.
At first, you may want to use a premade deck. I recommend downloading Ankidrone Starter Pack and learning from 1,000 to 3,000 cards from it. The deck has Japanese sentences on the front, English translations on the back. It also comes with native audio. You learn what the words mean and how to read them.
So you learn each word by itself, as a single unit, and over time your ability to predict kanji readings becomes stronger.