Prep your pan and oven. Line a 12-cup muffin tin with paper liners and lightly spray them. Preheat the oven to 350°F (175°C).
Combine dry ingredients. In a large bowl, whisk almond flour, coconut flour, baking powder, ginger, cinnamon, cloves, nutmeg, and salt until no clumps remain.
Whisk the wet ingredients. In a separate bowl, whisk eggs, almond milk, melted butter, vanilla, molasses (if using), and apple cider vinegar until smooth.
Sweeten the mix. Stir the granulated sweetener into the wet mixture, whisking to dissolve as much as possible. Taste and adjust sweetness if needed.
Bring it all together. Pour the wet ingredients into the dry.
Stir with a spatula until just combined. The batter will be thick but scoopable. If adding nuts or chocolate chips, fold them in now.
Portion the batter. Divide evenly among the muffin cups.
For nicely domed tops, fill each liner about 3/4 full and gently smooth the tops.
Bake. Place in the center of the oven and bake for 18–22 minutes, or until the tops are set and a toothpick comes out mostly clean with a few moist crumbs.
Cool properly. Let muffins cool in the pan for 10 minutes, then transfer to a wire rack to cool completely. This helps them firm up and prevents crumbling.
Optional glaze. For a quick keto glaze, mix 2 ounces softened cream cheese, 1 tablespoon heavy cream, 2–3 tablespoons powdered erythritol, and a splash of vanilla. Drizzle over cooled muffins.