Keto Pumpkin Cheesecake Muffins

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These keto pumpkin cheesecake muffins are fluffy and incredibly easy to make. The sweet cream cheese swirl takes them to the next level! They are packed with fall flavor and are only 2.9 grams of net carbs per muffin.

As soon as autumn is on the horizon, I get excited about keto pumpkin recipes. So when I got ready to make a batch of keto pumpkin muffins, I decided to take them up a notch and topped them with a cream cheese swirl.

We had these keto pumpkin cream cheese muffins as a breakfast treat for the last few days. And, I'll be honest with you, I also sneaked in a second one as an afternoon snack. They are that good!

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Why This Recipe Works
Ingredients
Instructions
Recipe Variations
Recipe FAQs
Storage
More Keto Pumpkin Recipes
Recipe

Why This Recipe Works

Moist yet fluffy crumb. The texture of these muffins is top notch.
Full of flavor. Yes, a good pumpkin muffin need plenty of pumpkin pie spice!
2 recipes in one. Literally, it's a mix between a muffin and a cheesecake. Perfect if you can't decide which you'd rather have right now.
Nut-free and gluten-free. This is a coconut flour recipe, which means it is suitable for anyone allergic to tree nuts.
Easy and quick. Suitable even for baking beginners, the muffins are ready in just 25 minutes.
Keto friendly. Just 2.9g net carbs per serve.

Ingredients

MUFFINS

Pumpkin puree. I used a canned pumpkin puree. However, you could also make homemade pumpkin puree.
Eggs. Should be large and room temperature.
Coconut flour. This healthy low carb flour is packed with nutrients and fiber.
Butter. Should be melted, then cooled.
Granulated sweetener. I used an erythritol monk fruit blend, but xylitol, allulose or pure erythritol all work well. Just be sure you are choosing a 1:1 sugar substitute.
Pumpkin pie spice mix. See further down in the post how to make your own.

CREAM CHEESE SWIRL

Cream cheese. Should be full fat and at room temperature. I like Philadelphia as it is smooth and creamy.
Heavy whipping cream. Makes the swirl even more silky and lush.
Powdered Sweetener. Don't use a granulated sweetener here as the result would be gritty. You can make your own powdered sweetener by blending granulated in a food processor.

Instructions

It is really easy to make keto pumpkin cream cheese muffins. Here are the basic steps.

For detailed instructions, scroll down to the recipe card.

STEP 1

Blend the eggs in a large mixing bowl until frothy and double in size. Then add the pumpkin puree and butter and mix to combine.

STEP 2

Add the all other ingredients except the walnuts and blend until smooth. Option to add a pinch of salt as well.

STEP 3

Fold in the walnuts. Then, scoop the mix into a muffin pan with paper liners.

STEP 4

Stir together the cream cheese filling ingredients in a small bowl using a spoon. Dollop the mix on top of the batter and swirl a little with a skewer or toothpick.

STEP 5

Bake until lightly browned on top and you can insert and remove a toothpick without it being sticky.

Expert Tips

Here are some tips to help you make perfect keto muffins.

#1 Whisk the eggs until frothy. You want to get as much air into the egg and pumpkin mix as possible. This will make the muffins fluffier. Mix with an electric blender for at least 2 minutes.

#2 Patience. Let the batter sit for a couple of minutes after blending so the coconut flour can absorb the moisture.

#3 Check for done-ness. Always check with a toothpick if your bakes are done on the inside. If your muffins aren't done yet but the cream cheese topping is browned enough, loosely place aluminium paper over the tops.

pumpkin cheesecake muffins in paper cases on a cooling rack

Recipe Variations

Almond flour. If you prefer baking with almond flour, use 1 1 /2 cups instead of the coconut flour.

Seed flour. In place of the coconut, you can also use seed flours. I recommend 1 cup sunflower seed flour mixed with ½ cup sesame seed flour. I grind these myself in a high speed blender, which is cheaper than buying them ready-made.

Dairy free. Swap out the butter for coconut oil when making the muffin batter. For the filling, use use coconut cream instead of dairy cream. There are dairy free cream cheeses by Daiya and Kite Hill which US based readers have recommended.

Recipe FAQs

How do I make my own pumpkin pie spice mix?

Mix together 1 ½ teaspoon ground cinnamon, ½ teaspoon each ginger and nutmeg and ¼ teaspoon each allspice and cloves. Makes 1 tablespoon.

Can I make this recipe in a loaf pan?

Yes. Line a 9x5 inch loaf pan with parchment paper. The oven time will increase to 60-65 minutes. Loosely place aluminium paper over the top once the cream cheese mixture is starting to brown and continue to bake until the inside is cooked fully.

Storage

Fridge: Store an airtight container in the refrigerator for up for 5 days.

Freezer: Pumpkin cream cheese muffins are freezer-friendly! Freeze in ziplock bags for up to 3 months and defrost on the counter or in the fridge.