Gluten-Free Cheesecake-Stuffed Pumpkin Cupcakes

These cupcakes have Isaiah’s name written all over them. If you have my book, Cooking for Isaiah, you may already be familiar with Isaiah′s Pumpkin Muffins with Crumble Topping (page 46). What you may not know is that Isaiah used to religiously eat pumpkin muffins (and muffin tops) from a café before he was diagnosed with gluten intolerance. The thought of him never walking into that café and eating those muffins again hurt.

And so began my uphill battle with developing a homemade gluten-free muffin that tasted and looked identical to the one he worshipped -the texture, the fluorescent orange color, the sugary sweet crumble topping. Recipe after recipe, I couldn′t figure out how to get it bright orange, so I went to the café and asked to see what ingredients were in the muffin. They pulled out a big, fat binder full of recipes and there it was, orange food coloring. I tossed the idea of adding artificial food coloring out the window and got back into the kitchen to do more testing. Finally, I nailed the perfect orange color (by using just the right amount of pumpkin puree), the perfect light texture, and, yes, the sugary sweet topping.

This cupcake goes a step further by adding Isaiah′s second favorite dessert into the mix: cheesecake. If you′re dairy free, just leave the cheesecake out and sprinkle the baked pumpkin cupcakes with confectioners′ sugar or top with your favorite dairy-free frosting.

[lt_recipe name=”Gluten-Free Cheesecake-Stuffed Pumpkin Cupcakes” servings=”12″ print=”yes” ingredients=”One 8-ounce package cream cheese, at room temperature ;½ cup confectioners’ sugar ;2 large eggs, plus 5 large egg whites ;2 teaspoons pure vanilla extract ;1½ cups Silvana’s Kitchen Gluten-Free All-Purpose Flour ;2 teaspoons pumpkin pie spice ;1½ teaspoons baking powder ;¾ teaspoon salt ;1 cup canned pumpkin puree ;1 cup granulated sugar ;½ cup vegetable oil ;1 cup light brown sugar ;Simmering water ;3 sticks (12 ounces) unsalted butter or vegan butter, cut into tablespoon-size pieces and chilled” ]Place a rack in the lower third of the oven and preheat to 350 °. Line a 12-cup muffin pan with baking liners. Using an electric mixer, beat the cream cheese and confectioners’ sugar for 3 minutes. Beat in 1 egg white and ½ teaspoon vanilla. ;In a bowl, whisk the flour, pumpkin pie spice, baking powder and ½ teaspoon salt. In another bowl, mix the pumpkin puree, 2 eggs, granulated sugar, oil and 1 teaspoon vanilla. Whisk in the flour mixture. Layer each muffin cup with some of the pumpkin batter, then the cream cheese mixture, then more of the batter. Bake until springy to the touch, about 25 minutes. Let cool. ;Using the electric mixer, beat the brown sugar, remaining 4 egg whites and remaining ¼ teaspoon salt. Fill a medium saucepan with enough simmering water to reach a depth of 1 inch and place the mixing bowl on top. Whisk the mixture until it registers 160 ° on an instant-read thermometer. Transfer the bowl back to the mixer and beat at high speed until fluffy, then lower the speed and beat to room temperature, about 5 minutes. Add the butter, 1 tablespoon at a time, then beat at high speed for 5 minutes. Beat in the remaining ½ teaspoon vanilla. Transfer the frosting to a pastry bag and pipe large rosettes on top of the cupcakes.[/lt_recipe]


  1. Just interested in what gf flour blend is recommended. There are so many to choose from. My husband works at a mill and I could get all of the different types of flour to mix together, but don’t know what to get or how to mix it. Would I do better to purchase a premixed flour blend? I have been Gluten Free since June. It is so overwhelming.

    • Hi Brandi,
      Hi Brandi,
      Try getting her cookbook, Cooking for Isaiah, in it, she has her own gluten-free flour blend recipe that works great with her recipes.

  2. Made these cupcakes with the flour mixture in the cookbook and they were delicious. Did not make icing as it seemed too complicated. Next I’m going to make these but bake in a bread loaf pan so it can be sliced.

  3. My husband was recently diagnosed with celiac, its been really tough figuring out what to make for him. I think he would love these. The cheese cake filling really puts it over the top for me 😉

  4. Silvana’s flour mixture, which can be found in her ‘Cooking for Isaiah’ Cookbook is by far the best blend I’ve used. . . by far. Thank you so much for sharing you and allowing us to glean from your talents!

  5. Fairly simple, didn’t make the frosting, but They came out great. My first time baking gluten-free. :] Thank you for sharing this treat.

  6. Everyone loved them at my work. I will be using this recipe quite often. All my friends said they couldnt believe it was Gluten Free. If you love, Cream cheese, and Pumpkin, This is a treat for you.

  7. Delicious! The recipe made more like 18-20 cupcakes though, not 12.

  8. Can this be made using regular flour?

  9. Hi Lisa, yes! My gluten-free flour blend substitutes with regular all-purpose flour cup for cup.

  10. Can you use self-rising flour? If so, would you use the same amount?

    • Hi Dana, yes, go ahead and substitute self-rising flour. Just omit the baking powder called for in my recipe above. Happy baking!

  11. My family loves your recipes. Thanks to you we don’t feel like were deprived. As a mom it can be such a challenge cooking gluten free for a family. Children, as you know, can be fussy. I as so thankful for your recipe book and the recipes you share on the internet. I will be sure to get your next book if one becomes available. Thanks again! Laurie

    • Hi Laurie! Thanks for writing and I’m so happy to hear that you and your family are loving the recipes! Talk soon, Silvana

  12. Silvana,
    What size scoop are you using to layer the cupcakes? It looks like a 3 T but that would be a lot of batter to have 9 T of batter in each well.
    I love the pumpkin muffin recipe in your book. It is a winner for sure. Actually I love your entire book. I haven’t tried one recipe that isn’t a keeper. I can’t wait for the next book to come out!

  13. Hi Silvana, You have me hooked! I am a bit of a prefectionist when it comes to whatever I do. I am also a frugal person, so I hate wasting money on ingredients that end up getting thrown out in the end. I always check the reviews before I bake something, but quite often all I read is how good something looks by people who haven’t actually made the recipe. One of my pet peeves. Like we all can’t already see how it looks. Lol. Also, I think some of the people who have tried some of the recipes have just forgotten what good tastes like. So anyway, I said all that to say, I was so pleasantly surprise at how good my pumpkin cupcakes turned out. My husband who usually refuses to eat much of my gluten free food was greatly disappointed when he heard that I had made them to take to a funeral dinner at the church. So I have been ordered to make another batch. :o) He loved them. Thank you! I had given up on doing much baking for myself, I try to watch my weight and having a whole batch of something sweet all to myself really isn’t a good thing. But, If I can make something good enough that others will eat it too, then I will. I made your frosting too. I turned out great. Thanks again. I will be back soon to try some more of your recipes, so please keep them coming.

    • Hi Cathy, thanks for your comment! I’m so happy you’re loving the pumpkin cupcakes. They’re definitely a family favorite here, too! Talk soon, Silvana

  14. These look great but I have one question. The gf flour mix I’m using does not have xanthan gum in it. How much would I use for this recipe. Thanks.

  15. Hi Silvana, I would love to make this recipe but in Australia we don’t have canned pumpkin puree or pumpkin spice mix. I have found a recipe online for the spice mix but I am wondering about the puree- is it literally just pureed pumpkin, or do I need to add anything to it if I puree it myself, also what consistency does it need to be as often it is very thick. Thank you.

  16. You copied this recipe, word for word, from Rachael Ray magazine in 2009. All you did was substitute gluten free flour. How can you claim it as your own?!