Preheat your oven to 375°F (190°C). Line a muffin tin with paper liners or grease it well.
In a large bowl, whisk together the flour, baking powder, salt, black pepper, and thyme.
In a separate bowl, mix the mashed squash, melted butter, eggs, and milk until smooth.
Add the wet ingredients to the dry ingredients and stir until just combined. Fold in the shredded cheddar cheese and green onions, if using.
Divide the batter evenly among the muffin cups.
Bake for 20-25 minutes, or until the muffins are golden brown and a toothpick inserted into the center comes out clean.
Let the muffins cool in the tin for 5 minutes before transferring to a wire rack to cool completely. Serve warm or at room temperature.
