1. Preheat oven to 350F. Line 16 cups of two 12-cup muffin tins with baking cups and lightly coat each with cooking spray.
2. Whisk together sugar, flours, baking soda, and salt in a large bowl. Whisk together milk, yogurt, eggs, and orange zest and juice in a medium bowl. Fold milk mixture into flour mixture, then gently fold in cranberries until combined.
3. Spoon batter into baking cups until each is three-quarters full. Sprinkle with almonds. Bake until a toothpick inserted into the center of each comes out clean, about 20 minutes. Transfer pans to wire racks, and let cool for 10 minutes. Turn out muffins onto racks and let cool completely.