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Pecan Cupcakes with Brown Butter Cream Cheese Icing

Let me tell you, this icing is SOOO amazingly good, you don’t even need the cupcake. But, when you combine these keto Pecan Cupcakes with Brown Butter Cream Cheese Icing, each bite is perfection, and I’ll show you just how to make these amazing keto cupcakes!

pecan cupcakes with brown butter cream cheese icing on a plate
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I’ve tried dozens of different keto cupcakes, and to be honest, most of them are just not good.

These ones, which I’ve perfected, are GREAT! They’re moist, tender, and don’t have any weird flavors from substitute sugars or other keto ingredients. And, when you’re craving an easy keto dessert recipe, this is the one to pick!

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This Keto Dessert Recipe Makes Six Cupcakes

Why six cupcakes?

I’m the only one doing keto in my house, and I don’t want to have a bunch of cupcakes lying around. I want some variety!

So, I formulated this recipe to make six cupcakes so that I can go on to another delicious keto dessert recipe sooner.

What is Brown Butter Icing?

Keto Brown Butter Cream Cheese Icing – ya, the name is a mouthful but you need a BIG name to explain the BIG flavors in this icing.

When you brown butter, you’re cooking the butter solids turning them brown in color. And, when you mix that with cream cheese and So Nourished sugar substitute, the flavors are rich, almost caramel-like, and not too sweet.

I can’t even explain to you how freaking good this icing is! Try it and drop a comment below to tell me how much you love it!

What You Need To Make This Keto Cupcake Recipe

They’re not hard to make at all, and you probably have everything you need on hand!

six keto pecan cupcakes with brown butter cream cheese icing on a light green plate

Ingredients to Make Keto Pecan Cupcakes

Ingredients to make Brown Butter Cream Cheese Icing

How to Make Brown Butter

When you make brown butter, you’re cooking the butter solids. To do this, start with your butter and a small skillet.

Melt the butter over medium heat then keep it on the heat. The butter will foam up. Stir it constantly.

Once the foaming goes down, watch for the butter solids to turn brown. It’ll only take a few minutes. Look for medium brown in color.

Remove the butter from the hot skillet as soon as it is done – the butter will continue to cook in the hot skillet and you could end up burning the butter.

How to Make Pecan Cupcakes with Brown Butter Cream Cheese Icing

  1. Mix the dry ingredients in a bowl.
  2. In another bowl, mix the wet ingredients.
  3. Combine the wet and dry ingredients and fill muffin cups. Bake until cooked!
  4. To make the icing, whip the cream cheese then add the sugar.
  5. To brown the butter, cook the butter in a skillet until the butter solids turn brown. Let cool.
  6. Add the cooled butter to the cream cheese / sugar mixture and whip until light and fluffy.
  7. Pipe icing onto the cooled cupcakes, and dig in!

Chef Jenn’s Tips

  • Don’t over-mix the cupcake batter – just blend it enough to combine and get out the big lumps.
  • Spray muffin cup liners with a bit of cooking spraycoconut flour can stick to paper liners.
  • Bake until golden brown on top and set in the middle when you poke it with a thin knife or toothpick
  • Let cupcakes cool COMPLETELY before icing or your icing will melt
  • Make sure your cream cheese is at room temperature before mixing or you’ll have lumps
  • Don’t burn the butter! See my instructions on making brown butter above
  • I tested this recipe with So Nourished powdered sugar but you can use your favorite

Are Keto Pecan Cupcakes with Brown Butter Cream Cheese Icing Freezer-Friendly?

Yes! You can totally freeze these easy keto low carb cupcakes. Simply store them in a freezer-friendly container and freeze them for up to three months.

Or, freeze them overnight, uncovered and unwrapped on a sheet pan. Then, wrap each tightly in plastic wrap and then store them in a freezer zipper-top bag.

To thaw, remove the cupcake and let stand on the counter for about 30 minutes until thawed and ready to enjoy.

Like This? Also Try:

Or check out this delish keto pecan pie!

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keto pecan cupcake with brown butter cream cheese icing on a plate, coffee cup in background
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Pecan Cupcakes

Moist, flavorful, and with an icing that's soo good you'll want to eat it by the spoonful, these keto Pecan Cupcakes with Brown Butter Cream Cheese Icing are going to become your new favorite!
Course Desserts
Cuisine American
Keyword cupcake, dessert, keto cupcake, keto dessert, nuts, pecans
Prep Time 15 minutes
Cook Time 15 minutes
Total Time 30 minutes
Servings 6
Calories 343kcal
Author Chef Jenn




  • In a bowl, combine the almond flour, coconut flour, xanthan gum, pecans, and baking powder.
  • In another larger bowl, whisk the eggs until well combined. Add the melted butter and mix well. Finally, add the vanilla.
  • Add the dry ingredients to the wet ingredients and mix well. Your batter should be thick but still runny.
  • Spray a muffin pan with cooking spray and fill 6 muffin cups with equal amounts of batter.

Bake at 350-F for about 15 minutes or until the cupcakes are set in the middle – a toothpick or knife should come out clean when inserted.

    To Make The Icing

    • Beat the cream cheese with electric beaters until creamy and smooth.
    • Add the butter to a small skillet. Melt the butter over medium heat. Continue to cook the butter until the foaming subsides, and you start to see brown flecks in the bottom of the skillet. Don’t burn the butter – medium to dark brown solids are what you’re looking for. Remove the butter from the heat and let cool.
    • When the butter is cool, add it to the cream cheese and beat with the beaters for 2-3 minutes.
    • Add the powdered sugar substitute and 2 tbsp heavy whipping cream. Beat until light and fluffy. Add another tbsp or two of heavy whipping cream if your icing is too thick.

      To assemble
    • Top the cooled cupcakes with the icing and enjoy!


    Serving: 1cupcake and 1/6 of the icing | Calories: 343kcal | Carbohydrates: 6g | Protein: 6g | Fat: 34g | Saturated Fat: 17g | Cholesterol: 150mg | Sodium: 317mg | Potassium: 90mg | Fiber: 3g | Sugar: 2g | Vitamin A: 919IU | Calcium: 88mg | Iron: 1mg | Net Carbohydrates: 3g

    A Note on Nutritional Information

    Nutritional information for this recipe is provided as a courtesy and is calculated based on available online ingredient information. It is only an approximate value. The accuracy of the nutritional information for any recipe on this site cannot be guaranteed. Erythritol carbs (sugar substitutes) are not included in the carbohydrate counts as they have been shown not to impact blood sugar, and they have zero calories and zero carbs. Net carbs are the total carbs minus fiber.

    How long do these take to bake?

    They take about 15-18 minutes to bake.

    Can this recipe be doubled?

    Yes, simply double all the ingredients and fill 12 muffin cups instead of six.

    How many carbs are in each cupcake?

    Each cupcake, with icing, is about 5 net carbs.

    For more fabulous recipes like keto casseroles and keto appetizers, check out Italian sausage parmigiana, keto grilled vegetables, keto corned beef hash, keto king ranch chicken, and keto Tex-Mex casseroles. And, don’t forget to check out even more keto desserts recipes!

    about jenn

    Hi, I’m Jenn!

    I’m a cookbook author (Keto Soup Cookbook and Keto Diabetic Cookbook and Meal Plan) as well as a retired chef, recipe developer, and writer of this blog (that’s a lot of hats!). I embarked on a journey to create foodie-worthy Keto-friendly meals that any home cook can be proud of! No matter if you’re low-carb, no-carb, dirty, or strict Keto, there are recipes in Keto Cooking Wins for you and your family. Read more...

    8 thoughts on “Pecan Cupcakes with Brown Butter Cream Cheese Icing”

    1. I love the look of these. Pecan is such a great flavor and I’m so happy they are Keto.

    2. I made these without the icing. I didn’t see any sweetener in the cupcake recipe, so I added some. They were delicious! Now I’m thinking next time I’ll add the icing and they will be even better. Definitely will make these again. Thanks!

      • You’re right! There’s a bit of sweetness happening naturally in the cupcakes, but to balance out the icing, I’ve left additional sweetener out of the cupcakes themselves. Do try the icing! It puts these cupcakes over the top!


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