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side angle shot of Lemon Cranberry Seed Cupcakes with Lemon Greek Yogurt Frosting on top parchment paper with cranberry seeds scattered on parchment and a wooden spoon filled with cranberry seeds in bottom right of shot. cloth napkin in background.
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5 from 1 vote

Lemon Cranberry Seed Cupcakes with Lemon Greek Yogurt Frosting

These light and fluffy lemon cupcakes are dotted with beautiful red cranberry seeds and topped with a lemon Greek yogurt frosting!
Prep Time5 mins
Cook Time15 mins
Yogurt Straining Time8 hrs
Course: Dessert
Cuisine: American
Servings: 12 cupcakes
Calories: 213kcal
Author: Ashley Boyd


Lemon Greek Yogurt Frosting

  • 2 cups whole milk Greek yogurt
  • 2 teaspoons lemon juice
  • ½ teaspoon lemon extract
  • 1 cup powdered sugar or Swerve confectioners
  • 1-2 tablespoons coconut flour to thicken frosting, optional

For Cupcakes


  • Very important - before you do anything you need to strain your yogurt overnight for the frosting! This ensures that your frosting will be sturdy enough. If you skip this step, the yogurt will contain too much liquid and you will end up with a runny mess on top of your cupcakes. To strain yogurt, place yogurt in a fine mesh strainer positioned over top of a bowl to catch the liquid. Place plastic wrap over top and refrigerate yogurt overnight.
  • In a large bowl, beat yogurt, lemon juice, lemon extract and powdered sweetener with an electric hand mixer until frosting thickens, 2-3 minutes. Add the coconut flour if you'd like the frosting a bit thicker and mix to combine. Refrigerate frosting while you bake cupcakes.
  • Preheat oven to 350 degrees F. Line a cupcake pan with liners and set aside.
  • In a large bowl, sift together flour, stevia or sweetener of choice, baking powder, and salt. Add cranberry seeds and whisk to combine.
  • In a separate medium bowl, beat together milk, eggs, oil, lemon juice, lemon zest and lemon extract until fully combined. Add wet ingredients to the bowl with the dry ingredients and mix with a rubber spatula until just combined.
  • Spoon batter into cupcake pan, filling each liner about two-thirds full. Bake cupcakes for 15-17 minutes or until a toothpick comes out with only a few moist crumbs. Allow cupcakes to cool completely before frosting.
  • Remove frosting from refrigerator and spoon it into a gallon ziploc bag. Snip the corner of the bag with scissors and pipe frosting onto cupcakes. Garnish cupcakes with lemon zest and cranberry seeds if desired and enjoy!


*see blog post above for important sweetener substitution tips
**poppy seeds can be substituted if you are able to find cranberry seeds
Greek yogurt frosting does not hold its shape as long as regular buttercream. I recommend frosting the cupcakes no more than 30 minutes before serving.


Serving: 1Cupcake | Calories: 213kcal | Carbohydrates: 31.2g | Protein: 5.3g | Fat: 8.3g | Saturated Fat: 1.7g | Cholesterol: 27mg | Sodium: 124mg | Potassium: 144mg | Fiber: 0.8g | Sugar: 10.2g | Calcium: 82mg | Iron: 1mg