Chia Seed and Quinoa Breakfast Muffins

Have leftover quinoa? Make these Chia Seed Quinoa Muffins — light, fluffy muffins made healthier with whole wheat flour, Greek yogurt, chia seeds, and naturally sweetened with honey.

Chia Seed Quinoa Muffins - close up

If you have cooked quinoa in the fridge, these muffins are a great way to use it up. They combine whole grains, protein-rich Greek yogurt and quinoa, omega-rich chia seeds, and a touch of honey for natural sweetness. The texture is tender and slightly hearty from the quinoa and whole wheat flour, while the almond milk and egg keep the crumb moist. These muffins are easy to prepare and make a convenient grab-and-go breakfast or snack.

Muffins on a plate

Chia Seed Quinoa Muffins

Summary: Light, fluffy, and nutritious muffins made with cooked quinoa, whole wheat and all-purpose flour, chia seeds, Greek yogurt, and honey. Perfect for breakfast, a snack, or to pack in lunches.

Prep Time: 5 mins

Cook Time: 25 mins

Total Time: 30 mins

Servings: 15 muffins

Freshly baked chia quinoa muffins

Ingredients

  • 2 cups cooked quinoa
  • 1/4 cup plain Greek yogurt
  • 1 cup whole wheat flour
  • 1 cup all-purpose flour
  • 1 1/2 tsp baking powder
  • 1 tsp salt
  • 2 Tbsp chia seeds
  • 3/4 cup unsweetened almond milk (or other milk of choice)
  • 1 egg
  • 1/3 cup honey
  • 1 tsp vanilla extract

Instructions

  1. Preheat the oven to 350°F (175°C). Grease a muffin tin or line it with paper liners.
  2. If you haven’t already, cook quinoa according to package directions and allow it to cool for about 5 minutes so it’s not steaming hot when added to the batter.
  3. In a medium bowl, combine the cooked quinoa, whole wheat flour, all-purpose flour, baking powder, salt, and chia seeds. Stir to distribute ingredients evenly.
  4. In a smaller bowl, whisk together the almond milk, egg, Greek yogurt, honey, and vanilla extract until smooth.
  5. Pour the wet ingredients into the dry quinoa mixture and gently stir until just combined. Avoid overmixing; the batter should be evenly moistened but not beaten excessively.
  6. Divide the batter evenly among the prepared muffin cups.
  7. Bake for about 25–30 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
  8. Allow the muffins to cool in the tin for 5 minutes, then transfer to a wire rack to cool slightly before serving.

Nutrition (per muffin)

Serving: 1 muffin | Calories: 110 kcal | Carbohydrates: 20.6 g | Protein: 4 g | Fat: 1.5 g | Saturated Fat: 0.2 g | Fiber: 2.1 g | Sugar: 2.7 g

Nutrition information is automatically calculated and should be used as an approximation.

Notes and Tips

These chia seed quinoa muffins are versatile. Add-ins like blueberries, chopped apples, mashed banana, or a handful of nuts will work well — fold them into the batter gently before dividing into tins. For a little extra sweetness on top, brush the warm muffins with a thin layer of extra honey or sprinkle with oats.

Storage: Store cooled muffins in an airtight container at room temperature for a day or two, refrigerate for up to a week, or freeze for longer storage. To reheat, warm gently in the microwave for 15–30 seconds or in a 325°F oven for a few minutes.

Dietary swaps: Use a non-dairy yogurt if you need the recipe to be dairy-free, and choose a suitable non-dairy milk. To reduce added sugar, reduce the honey slightly or replace with a mashed ripe banana if you prefer.

Serving suggestions: Enjoy these muffins for breakfast with a cup of yogurt or tea, pack one for a snack on the go, or serve alongside fresh fruit for a light brunch.

If you have leftover quinoa, this recipe is a simple, satisfying way to turn it into a nutritious, portable treat. The combination of quinoa and Greek yogurt adds protein and texture, while chia seeds provide a pleasant crunch and extra fiber.