Preheat the oven to 350°F (175°C). Lightly grease a mini muffin tin or line with silicone cups to prevent sticking.
Cook the sausage. In a skillet over medium heat, break up the sausage and cook until browned and no longer pink.
Drain excess grease and let it cool slightly.
Whisk the wet ingredients. In a large bowl, whisk the eggs until smooth. Add the softened cream cheese and whisk again until mostly blended. Small specks are fine.
Add the dry ingredients. Stir in almond flour, baking powder, garlic powder, onion powder, black pepper, and a pinch of salt.
Mix until combined.
Fold in the sausage and cheese. Add the cooked sausage and shredded cheddar. If using add-ins like green onions or jalapeños, fold them in now.
Fill the muffin cups. Spoon the mixture into the mini muffin wells, filling each about 3/4 full. Tap the pan gently to level.
Bake. Place on the center rack and bake for 16–20 minutes, or until the tops are set and lightly golden.
A toothpick should come out with just a few moist crumbs.
Cool and release. Let the bites rest in the pan for 5 minutes, then run a small knife around the edges and lift them out. Serve warm or cool completely for storage.