You kind of just get a feel for it after a while and can guess with pretty good accuracy whenever you encounter a new usage of a kanji that you’ve learned before. In general, the rules that I use are:
- Government or legal texts - Jukugo galore, almost everything is going to be onyomi. This is because back in the day, Chinese was the lingua franca. Even today, using more onyomi words has a feeling of being more “academic” and “smart-sounding.”
- Folk custom related or other traditional writing - Almost always kunyomi. Even any jukugos will be given kunyomi. They also typically hide pronunciations that would be covered by okurigana in the modern age. For example, yama-no-te is frequently written 山手 without the の.
- Names (people and places) - Onyomi is typically the exception. Vast majority of the time, you’re safe using kunyomi.
- There’s also a set of kanji that just have one pronunciation in major use. After you see it enough, you just kind of know that it’s only pronounced this one way.
My recommendation is just to learn the sounds of vocabulary words, independent of their kanji. Once you do that, you tie the sound to the meaning, rather than having to go through the characters used.