Preheat the oven to 325 degrees Fahrenheit. Line a large baking sheet with parchment paper.
Combine peanuts, rice Chex, and pretzels in a medium bowl. (Cheese puffs will be added at the very end.)
Melt butter in a glass measuring cup or small microwavable bowl. Add spices, nutritional yeast, and coconut sugar to the melted butter. Whisk to combine.
Pour liquid mixture over the dry ingredients. Gently stir mixture until most pieces are coated. Spread mixture into an even layer on baking sheet.
Bake for 15 minutes. Remove pan halfway through cooking, stir, and return to oven for remaining cook time.
Allow Chex mix to cool before adding cheese puffs. Store in an airtight container.