Yes, you can probably let your food cool first, though you want to minimize the time it’s at room temperature. Alternatively, you can immediately freeze the hot food into bricks, and then vacuum seal it which will make it retain its shape better.

Anaerobic bacteria like the one that causes botulism cannot grow in the presence of oxygen, so if you leave your food out on the counter, it won’t be able to grow.

However, once you vacuum seal it and there’s no oxygen, it can grow if it’s there in the first place or acquired the bacteria while it was cooling. Generally, you want to freeze or refrigerate the food as soon as possible to reduce the chance of bacterial contamination.

Since these bacteria are soil bacteria, they are more likely to be on vegetables in the soil like garlic, onion, and mushrooms.

Most importantly, follow the “Guidelines for Vacuum Packaging” section of your manual since it gives explicit instructions on how to vacuum pack various foods.