Heat oil in a large skillet over medium heat. Add onion and bell pepper; cook, stirring often, until the onion is tender, about 5 minutes. Transfer to a large bowl and let cool for 10 minutes.
Meanwhile, preheat oven to 400°F Coat a mini-muffin pan with cooking spray.
Whisk whole-wheat pastry flour, all-purpose flour, baking powder, oregano, sugar, garlic powder and salt in a medium bowl.
Stir milk, feta, egg, tomato paste and olives into the onion mixture. Make a well in the dry ingredients; add the wet ingredients and stir until just combined. Fill the prepared muffin cups two-thirds full.
Bake the muffins until lightly browned, 13 to 15 minutes. Cool in the pan for 5 minutes before turning out onto a wire rack. Serve warm or at room temperature.