This will get better with exposure to more vocab; you’ll start to get a knack for patterns which tell you whether to use on’yomi or kun’yomi. I was definitely still memorizing the vocab readings on a case-by-case basis at level 3 (and also waited an extra week to crush leeches before subscribing) so it’s not something to be ashamed of and definitely not directly comparable to higher-level members’ accuracies.
Basically, verbs (non-する) with okurigana will always use kunyomi readings, as will い-adjectives and various nouns/na-adjectives. Kanji compounds with 2+ kanji (including する verbs) will usually use on’yomi, and 1-kanji words will usually use kun’yomi. These last two have exceptions you’ll still have to memorize case-by-case (by relying on mnemonics) but it’s better than a blank slate for every word.
Also on levels 1-3 there are the つ-counters and 日-counters which have exceptional (kunyomi) readings you just have to slog through. Those drop off after a few levels.