Preheat oven to 350 degrees F (175 degrees C). Place spaghetti squash cut-side down in a shallow baking pan. Add about 1 inch water.

Bake in the preheated oven until flesh is soft, about 1 hour 25 minutes. Scoop out flesh with a spoon and measure out 2 cups; refrigerate until cool, 15 to 20 minutes.

Increase oven temperature to 400 degrees F (200 degrees C). Lightly grease two 12-cup muffin tins.

Whisk flour, sugar, baking powder, cinnamon, nutmeg, ginger, allspice, and salt together in a large bowl.

Mix milk, eggs, butter, and vanilla extract together in a separate bowl. Stir in spaghetti squash. Fold the squash mixture into the flour mixture just until moistened.

Spoon batter into the prepared muffin tins, filling each cup halfway.

Bake in the preheated oven until a toothpick inserted into the center comes out clean, about 25 minutes. Remove from muffin tins and cool on wire racks.