I absolutely love Boston Cream Pie!
But I haven’t had it in many years because I’ve never seen a gluten free version in any bakery. Plus this kind of cake is usually loaded with sugar and instant pudding with food coloring in the center. No thanks! I prefer to stick to real food ingredients and no refined sugar.
My Tiny Love and I have birthdays back to back. This year she asked for Strawberry Cake, so I knew I had one cake to make first. For my birthday, I decided to make cupcakes instead of cake. I was determined to make my favorite … Boston Cream Pie … in cupcake form.
Lately I have been only baking with my new favorite flour, Otto’s Cassava Flour. I love that cassava flour is a resistant starch when eaten cool {resistant starch = prebiotics that feed probiotics + supports digestion and the gut}.
I really love that I don’t have to add extra gums or other flours to make baked goods stay together and not crumble. This flour works so well as a 1:1 flour substitute in most recipes.
I was so excited to eat these cupcakes on my birthday. My husband made me a lovely dinner, which was perfect and so good … I may have enjoyed a bit of the cupcake filling first. I couldn’t resist.
These grain free vanilla cupcakes are filled with homemade vanilla custard and topped with beautiful chocolate ganache. So good!
The cupcakes only lasted until the next morning. We devoured half of them on my birthday and the rest the next day for breakfast. Yes, I ate some with my breakfast. And I enjoyed every single bite.
Boston Cream Pie Cupcakes
YOU WILL NEED: Muffin Pan, Unbleached Muffin Wrappers, Mixing Bowls, Hand Mixer, Medium Saucepan, Whisk

Boston Cream Pie Cupcakes {Grain Free}
These grain free vanilla cupcakes are filled with homemade vanilla custard and topped with beautiful chocolate ganache. So good!
Ingredients
For the Vanilla Cupcakes:
- 8 tablespoons pasture butter, room temperature
- 3/4 cup maple sugar
- 2 teaspoons vanilla extract
- 3 pastured or organic eggs, room temperature
- 1 1/2 cups Cassava Flour (<-- this is the only cassava flour I use and recommend)
- 2 tablespoons grass-fed collagen (<-- this is the only grass-fed collagen I use and recommend)
- 2 teaspoons baking powder
- 1/2 teaspoon Celtic sea salt (<-- this is my favorite sea salt)
- 2/3 cup organic buttermilk, room temperature
For the Vanilla Custard Filling:
- 2 cups organic whole milk
- 3 pastured or organic egg yolks
- 1/3 cup light colored honey {not wildflower - I used creamed clover}
- 4 tablespoons organic non-GMO corn starch
- 1 tablespoon pasture butter
- 1 1/2 teaspoons vanilla extract
For the Chocolate Ganache:
- 1 1/2 cups allergy-friendly chocolate chips
- 2 tablespoons pasture butter
- 1/4 teaspoon Celtic sea salt
Instructions
To Make the Vanilla Cupcakes:
- Preheat the oven to 350 degrees F.
- In a mixing bowl, combine cassava flour, collagen, baking powder and sea salt. Stir and set aside.
- In a large mixing bowl, cream softened butter and maple sugar with a hand-held mixer. Add vanilla and mix just until combined.
- Add eggs and mix just until combined.
- Alternate adding flour mixture and buttermilk in two batches, stirring with the mixer just until combined. Do not over mix.
- Evenly distribute the cupcake batter, pouring into cupcake wrappers.
- Bake for 17-20 minutes or until a toothpick inserted into the center comes out with only a few moist crumbs {not wet}. Do not over bake. [Note: I checked mine at 15 minutes and they were done at 17 minutes. All ovens bake differently, so make sure to check them around 15 minutes to gauge doneness.]
- Allow to rest in the muffin pan for about 5 minutes then carefully remove cupcakes from muffin pan and place on a cooling rack. Allow cupcakes to cool completely.
To Make the Vanilla Custard:
- In a medium size mixing bowl, beat the egg yolks. Add the milk and stir to combine.
- In a medium size saucepan over medium-low heat, add honey and cornstarch. Stir to combine then slowly add egg-milk mixture, whisking to prevent lumps.
- Whisking constantly, continue cooking over medium-low heat until a low boil starts and custard starts to thicken. Once it starts to boil, allow boil for about 1 minute then immediately remove from heat. The custard should be thick, like pudding consistency.
- Add butter and vanilla extract. Stir to combine until butter has melted. Pour into a glass bowl {I used a shallow glass pie dish} and store the custard in the refrigerator until chilled {at least 1 hour}.
To Make the Chocolate Ganache:
- In a small saucepan, gently heat the chocolate chips, butter and sea salt over low heat, stirring occasionally until fully melted and glossy. Set aside to cool slightly.
To Assemble the Cupcakes:
- When cupcakes are fully cooled, use a paring knife to carve out a small portion in the center of the top of the cupcakes {making a cone shape}. I removed about 2 tablespoons of the cupcake center - place those excess pieces in a mason jar and store in the freezer for later use {or just nibble on them now}.
- Evenly distribute tablespoonfuls of the cold vanilla custard into the carved out center tops.
- When the cupcakes are filled, spoon the ganache over the tops of the cupcakes, fully covering the top. If needed, tilt the cupcakes to the side to allow excess ganache to fall off.
- Let the ganache set up before serving. If you need to speed up the process, place cupcakes in the refrigerator for about 5 minutes.
Notes
-I have not tried making these with other sweeteners. I do not recommend replacing the maple sugar with honey or maple syrup since this will change the texture of the cupcakes. It's possible other unrefined sweeteners like coconut sugar or Sucanat would work too, but please note the color of the batter will be darker.
-It's important for all ingredients to be room temperature. If you need to remove the chill from the eggs really quick, place them in a bowl of warm/hot {not boiling} water for about 7 minutes. This will help bring them to room temperature fast.
* I highly recommend using the collagen in the cupcakes. It helps provide a really lovely "soft" texture to the cupcakes. It's also gut-healing and protein-packed, so it adds a health benefit as well. It cannot be swapped with grass-fed gelatin - while both gelatin and collagen provide the same health benefits, they are not interchangeable in this recipe. You can choose to omit the collagen - it will change the texture a bit, but not drastically. I've linked to my favorite collagen brand in the ingredients - I love the company, the quality and the price point is the best I have found. It's also the brand that my family uses daily for health purposes.
STORAGE: These cupcakes are best eaten the same day but can be stored in an airtight container in the refrigerator for up to 2 days.
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Nutrition Information:
Yield: 10 Serving Size: 1Amount Per Serving:Calories: 496Total Fat: 26gSaturated Fat: 15gTrans Fat: 1gUnsaturated Fat: 9gCholesterol: 177mgSodium: 477mgCarbohydrates: 60gFiber: 2gSugar: 38gProtein: 9g
This nutritional information was auto-generated based on serving size, number of servings, and typical information for the ingredients listed. To obtain the most accurate representation of the nutritional information in a given recipe, please calculate the nutritional information with the actual ingredients and amounts used, using your preferred nutrition calculator. Under no circumstances shall the this website and the author be responsible for any loss or damage resulting for your reliance on the given nutritional information. You are solely responsible for ensuring that any nutritional information provided is accurate, complete, and useful.
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These cupcakes look heavenly! I love boston cream pie, and I also love cassava flour! I love that the ingredients are all natural and not artificial!
Thanks so much Bethany! xo 🙂
Hi there! My hubby loves anything Boston Cream related, so I’m excited to make these cupcakes for him for Valentine’s Day. They sound amazing! However, I had a couple questions. Do I really need casava flour? I’ve never heard of that one and I already have a few different grain free flours, such as coconut and almond. Would one of those work? Also, what is the deal with the hydrolyzed collagen. That is another thing I haven’t heard of before. Could you substitute grass fed gelatin? Thanks in advance! 🙂
Hi Michelle, yes, this recipe does call for Otto’s cassava flour. I highly recommend this flour if you’ve never tried it before – it’s my favorite grain free flour. Check out this post my friend wrote, she goes into more detail about the health benefits of cassava flour, make sure to scroll down to the bottom of the post too – she discuses more about it in terms of digestion. You could absolutely try almond flour, but I can’t guarantee the results since I haven’t made these with nut flours. I wouldn’t recommend coconut flour since that flour is not one that can be swapped 1:1 for flours … it requires a lot more liquid and usually more eggs. Collagen is the same as gelatin except it is cold water soluble, so it will dissolve in any liquid, gelatin won’t. They cannot be substituted/swapped in this recipe. Most grass-fed gelatin companies also make collagen. I link to the brand I use and highly recommend in the ingredients. I really recommend adding the collagen to the cupcakes because it helps provide a really lovely “soft” texture {plus adds more protein and it’s gut-healing too}. You can leave it out altogether if you prefer. I’ll edit my post to make it optional. Hope that helps!
Thank you so much for replying so quickly! Greatly appreciated!!! 🙂 I will definitely try the cassava flour!
I hope that helped Michelle 🙂
OH MY!! Looks amazing! I haven’t tried cassava flour yet but keep meaning to order some. This is great inspiration!
Thanks so much Tina! I hope you get to order some, it’s awesome flour 🙂
Bet can’t eat just one.
LOL … truth! 😉
I love this recipe! I also love that you are enjoying cassava flour so much. I have made tortillas with it and loved it. Making brownies this week!
Thanks Linda 🙂 xo I want to make tortillas next, yum! Enjoy the brownies!
I have some cassava flour in my pantry. I’m probably going to have to try these. They look SO delicious! 🙂
They have chocolate 😉 Can’t resist that! xo
wow, these look incredible! And I love that you used all good ingredients! I cannot wait to try my hand at these!
Thanks Kristen! 🙂
I love boston cream pie i bet this recipe is amazing!
Thanks Kristina! 🙂 I love it too, all of the components just go so well together!
These look fantastic! I am a chocoholic and sweets person. I can see myself really enjoying these cupcakes. Yum!
Thanks Christine! Me too 😉
I still need to get my hands on cassava flour! These look amazing as always and I can’t wait to try them. They’re really cute too!
Thanks Tash! Otto’s make the best cassava flour, I just love it 🙂
Wow… these may warrant a trip back out to the store WITH my toddler. And, that’s really saying something. YUM!
LOL I hear you, shopping with the kiddos can be … well … interesting. 🙂
Those look amazing! Boston Cream Pie is one of my favorite too! I’m glad you were able to make one Grain Free! Yum!
Thanks Elaine! Isn’t Boston Cream Pie just the best? 🙂
These look absolutely amazing! What a wonderful dessert! Saving for later!
Thanks so much Tiffany!
Great recipe. You make it seem so simple and I’m very interested in a bunch of these new ingredients that i have never heard of.
Thanks John! I know there are a lot of steps to this one, but it really is pretty simple. I love baking with Otto’s cassava flour now, my favorite dry unrefined sweetener is maple sugar – it’s so delicious, and the collagen … well, it’s just awesome stuff {plus adds a gut healing and protein boost}.
I’ve actually never had Boston Cream Pie…crazy I know… but these look really good!
Oh it’s such a treat Jennifer! I hope you get to at some point 🙂
These look sooo special!! I LOVE custard, cake and chocolate together, too! Pinned and yummed and sharing!
Thank you so much Megan! xo And thank you for the pin!
Oh but that custard! These are so special Emily! Thank you for the great idea!
Thanks Renee … I love the custard, the little bite inside is such a tease. 🙂
I love Boston creme pie. These cupcakes look so amazing. How do I sub for the buttermilk? I don’t think I can handle it.
How do you only eat one?
I don’t think you can only just eat one 😉 I’m not sure Anna, I haven’t tried this recipe with anything other than buttermilk.
I just got a bag of Otto’s! I don’t know if I should make these though…I’m afraid I’ll finish the whole pan or my hubby would and he definitely don’t need extra sugar! These looooook amazinnnnng!
LOL 🙂 I’m so excited you got some Otto’s, it’s awesome stuff!
Now that’s the way to celebrate, they look amazing!
Thanks Sylvie! 🙂
These look delicious! There are a few ingredients I have not worked with before, but I’m definitely pinning this for when I’m feeling adventurous 🙂
Thanks Chrystie 🙂 Appreciate the pin!
Oh my, that ganache! These cupcakes look really good!
Thanks so much Bethany! xo
Can you change arrowroot for corn starch?
Hi Marybeth, I haven’t used arrowroot in this recipe, so I’m not sure. Sometimes arrowroot works in “puddings/custards” but arrowroot can also be finicky with heat and dairy. So, I can’t say for sure but if you try it let me know 🙂
Holy moly! I am in loveeeee! These look insane! My mom would adore them too if she and I could actually eat them! WOMP! But thank you for the visual food porn! 😉
LOL thanks! 🙂 They’re so yummy!