Blueberry Vanilla Cupcakes with Blueberry Ganache

Blueberry Vanilla Cupcakes with Blueberry Ganache have a vanilla cupcake base mixed with blueberry puree and a blueberry ganache frosting. If you love blueberries, these are the cupcakes for you!

Blueberry Vanilla Cupcakes with Blueberry Ganache

Today is my last data presentation to my lab before we move, and my last day in the lab is tomorrow. It’s a bittersweet transition. As much as I look forward to starting a new project in a slightly different field of study, I will miss my boss and coworkers. The saying “beginnings are scary and endings are sad” flashes through my mind a lot, because I am beginning a new chapter of my life and ending a previous one.

These last few days I have been cleaning out all of my stuff from the lab, and it’s actually been a pretty liberating experience – throwing out SO much makes me feel like I am starting with a clean slate, and that’s always a good thing.  

Blueberry Vanilla Cupcakes with Blueberry Ganache

Because this is my last lab meeting, I thought long and hard about what treat I wanted to take. If you remember, my lab gave me my KitchenAid mixer as a gift for finishing my PhD, so I try to thank them with baked goods as often as I can!

Developing the Recipe

I have been trying to use up what I have in the freezer, so the abundance of Michigan blueberries seemed like a good place to start. I decided to combine components of two recipes I’ve made in the past – adapting the Blackberry Vanilla Cupcakes to include blueberries instead, and topping them with blueberry ganache. Ever since I first made the blueberry ganache it’s been on my mind. It’s truly a unique flavor; as Bob put it, “the blueberries add such a brightness to the ganache.” 🙂 Someone’s been watching too much Top Chef Masters and Chopped!  

I can’t report on how the lab liked these because they haven’t tried them yet! I’ll update the post with the results later. I gave Bob his usual taste-testing cupcake, and he loved it! He said the cupcake was nice and fluffy, and you can tell from the above quote that he likes the ganache!

I had a bite of his, and it was great. Love, love, love this ganache. I HIGHLY recommend trying it – soon! I am already brainstorming up different ways to use it. As I was putting the ganache in the fridge to cool, I spotted some strawberries, so I dipped some in the ganache and put them on a separate plate to cool – awesome!  

Recipe Notes

It’s important not to overfill the cupcake wells with batter. The cupcakes tend to overflow if filled too high, and they bake up with very flat tops rather than rounded. I think if you fill 2/3 of the cup you’ll have much better results than I did. The edges stuck to my pan and each one looks like I chewed around the entire cupcake . . . hopefully my coworkers won’t mind!  

The ganache needs to be chilled in the refrigerator for 1 to 2 hours until it reaches a pipeable consistency. I have the recipe structured that the cupcakes are made first and then the ganache. I actually made the cupcakes the night before the ganache and stored them in a covered cake pan. Another option is to make the ganache first and let it chill while you make the cupcakes. You will want to make sure the cupcakes are completely cool before piping the ganache on top.

Gluten Free Blueberry Vanilla Cupcakes with Blueberry Ganache

I haven’t tried it myself, but I have had good luck using Bob’s Red Mill Gluten Free 1 to 1 Baking Flour in place of all purpose in many cakes recipes.

Looking for More Cupcake Recipes?

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Mexican Chocolate Black Bottom Cupcakes
Carrot Cupcakes with Cream Cheese Frosting
Tres Leches Coconut Cupcakes with Dulce de Leche Buttercream
Samoa Cupcakes with Easy Dulce de Leche Buttercream
Baby Bluebird Cupcakes

Blueberry Vanilla Cupcakes with Blueberry Ganache

Blueberry Vanilla Cupcakes with Blueberry Ganache

Vanilla cupcakes with a blueberry puree mixed in, topped with a blueberry ganache.
Prep Time 40 minutes
Cook Time 20 minutes
Chill Time 2 hours
Total Time 3 hours
Course Dessert
Cuisine American
Servings 14 or more cupcakes


  • two 12-cup cupcake pans


For the Blueberry Puree:

  • 1 cup frozen blueberries (see note)

For the Cupcakes:

  • 1 cup flour
  • 2 teaspoons baking powder
  • 1 teaspoon salt
  • 6 tablespoons unsalted butter (at room temperature)
  • 1 cup sugar
  • 1 teaspoon vanilla extract
  • 2 eggs (at room temperature)
  • 1/2 cup milk

For the Ganache:

  • 12 ounces best-quality semisweet chocolate chips (such as Ghirardelli)
  • 2 cups frozen blueberries
  • 1/2 cup sugar
  • 1/2 cup heavy cream
  • 4 tablespoons unsalted butter


Make the Blueberry Puree:

  • Puree the blueberries in a food processor or blender. Pour the puree into a fine-mesh sieve set over a bowl. To facilitate straining the puree, whisk the blueberry mixture as you strain it through the sieve. You should get about 1/2 cup of puree. Set aside and make the cupcake batter.

Make the Cupcakes:

  • Preheat the oven to 350 degrees F and line two 12-cup cupcake pans with paper liners.
  • In a small bowl, sift together flour, baking powder, and salt. Set aside.
  • In a liquid measuring cup, whisk together the milk and blueberry puree. Set aside.
  • In the bowl of stand mixer, cream together the butter and sugar on medium speed until light and fluffy.
  • Add the eggs one at a time, scraping down the bowl between additions, add the vanilla extract.
  • Add half of the dry ingredients to the large bowl and mix on low speed until just combined. Add the strained blueberry puree, and mix on low until just combined. Mix in the remaining dry ingredients on low speed until just incorporated. Do not overmix.
  • Divide the batter evenly between the cupcakes, filling 2/3 full.
  • Bake 12 – 15 minutes or until a toothpick inserted in the center comes out clean. Allow to cool in the pan 10 – 15 minutes. Transfer to a wire rack and allow to cool completely.

Make the Ganache:

  • Place the chocolate chips in a large mixing bowl and set aside.
  • Place the blueberries and sugar in a small saucepan over medium heat. Cook and stir until the mixture becomes sauce-like and bubbly. Pour into a sieve or strainer that is placed over the bowl containing the chocolate chips to catch the blueberry liquid. Discard the remaining blueberries.
  • Bring the cream and butter to just below boiling in a small saucepan over medium heat. Pour the hot mixture over the chocolate and let stand for 30 seconds. Stir the mixture until smooth.
  • In order to achieve a consistency desired for piping, cover bowl of ganache with plastic wrap and chill until piping consistency is reached (approximately 1 – 2 hours).
  • Pipe ganache as desired.


You may substitute fresh blueberries in place of frozen.  You may need more than 1 cup to get 1/2 cup of puree, which is what 1 cup of frozen blueberries yields.
Source:  Cupcake recipe adapted from Coconut & Lime, ganache adapted from Picky Palate
You’re Gonna Bake It After All
Keyword blueberry, cupcake, dessert, vegetarian

11 thoughts on “Blueberry Vanilla Cupcakes with Blueberry Ganache”

  • What an interesting addition to ganache! I don't think I have ever heard of anything like it.
    These look fantastic. Good luck on this new stage of life. I agree it is hard to change everything, but here's hoping things turn out great!

  • Good luck in your new lab! I work for Thermo Fisher Scientific, so am always supportive of lab folk. 🙂 I found your blog while I was Googling "Monkey Bread", and I really enjoy your recipes and your style of writing. Thanks!

  • Aww, I can't believe your last day in lab is already here. I remember it was a bit of a bittersweet time, but I was so excited to start thinking about something new 🙂

    I can just imagine how much your lab mates loved these cupcakes! The blueberry ganache sounds so unique and indulgent!

  • I don't think your co-workers will mind! These look positively scrumptious. Their going to miss you – and your treats!

  • These look great. I just happened upon your blog and I really like all the recipes. I'm a fan. I also have a dedicated baking blog, if you ever need inspiration. Thanks for sharing.

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