Prep the oven and pan: Preheat oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or silicone cups. Lightly grease if needed.
Whisk the dry ingredients: In a large bowl, combine 2 cups almond flour, 2 tablespoons coconut flour, 1/2 cup keto sweetener, 2 teaspoons baking powder, 1 1/2 teaspoons cinnamon, 1/4 teaspoon nutmeg, 1/4 teaspoon ground ginger, and 1/4 teaspoon salt.
Mix well so the leavening and spices are evenly distributed.
Mix the wet ingredients: In a separate bowl, whisk 3 large eggs, 1/3 cup unsweetened almond milk, 1/3 cup melted butter or coconut oil, 1 teaspoon vanilla extract, and 1/4 cup sour cream or full-fat Greek yogurt until smooth.
Combine the batters: Pour the wet ingredients into the dry and stir until just combined. The batter will be thick—this is normal.
Add the carrot and mix-ins: Fold in 3/4 to 1 cup finely grated carrot (squeezed dry in a paper towel). Add 1/3 cup chopped walnuts or pecans if using.
Avoid overmixing.
Fill the muffin cups: Divide the batter evenly among the 12 cups. They can be quite full; keto muffins don’t rise as high as wheat flour muffins.
Bake: Bake for 18–22 minutes, until the tops are set and a toothpick comes out mostly clean with a few moist crumbs.
Cool: Let muffins cool in the pan for 5 minutes, then move to a wire rack to cool completely. Almond flour muffins firm up as they cool.
Optional cream cheese topping: Beat 4 ounces softened cream cheese with 2–3 tablespoons powdered keto sweetener, 1 teaspoon vanilla, and 1–2 tablespoons heavy cream until smooth.
Spread on cooled muffins.