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Tis the Season To FALL In Love With This Pumpkin Cream Cheese Muffin!

Tis the Season To FALL In Love With This Pumpkin Cream Cheese Muffin!
Jump to Pumpkin Muffin Recipe

The days have officially begun to grow shorter, and even though here in South Dakota the punishing heat is raging on, I have begun to feel the Fall vibes creeping in! Soon we will be able to walk outside comfortably again, and the insect population will stop thriving so vivaciously. People will begin to bring out their decorative gourds, and even more exciting are the recipes to be had that are made using the hallmark gourd of the Fall season, the PUMPKIN! If you can’t tell, I am not a summer person 😂 To celebrate the beginning of this joyous season I bring you my delectable keto pumpkin muffins with a cream cheese filling topped with crunchy candied pecans!

Pumpkin Muffins With Cream Cheese Filling from

Why You Will Love This Pumpkin Muffin

  • Only 1.8 grams of net carbs per serving!
  • Pumpkin spice in the muffin batter gives spicy, cinnamon, Fall vibes all day!
  • The cheese cake like filling makes this muffin teeter on the verge of being an indulgent dessert.
  • The crunchy candies pecans are the unsung hero in this muffin recipe! You will want to bake a tray just to snack on!

What You Will Need To Make These Pumpkin Muffins

  • Baking Sheet
  • Cutting board
  • Knife
  • 1 small, 2 large mixing bowls
  • Spoon
  • Whisk
  • Measuring cups
  • Measuring spoons
  • Muffin liners
  • Muffin tin
  • Large Ziploc bag and scissors (or a pastry bag)
  • wire rack
Ingredients for Keto Pumpkin Muffins from

Let’s Talk About Flour Blends

I have been experimenting a lot with different flour blends to help me achieve the best texture, crumb, and overall quality of low-carb baked goods. I am really excited to publish my first recipe using this flour blend! It is a combination of lupin flour, almond flour, coconut flour, vital wheat gluten, oat fiber, xanthan gum, and just a little bit of erythritol. These ingredients combined have produced the closest thing to glutenous flour so far, and coming in at 5 net carbs per cup, this flour blend can be used in keto and low-carb baked goods!

What is Lupin Flour? Lupin flour is made from lupin beans a plant in the legume family similar to the peanut or soybean. Lupin flour has a neutral and slightly starchy taste, and it has a soft and fluffy texture very similar to wheat flour. The fluffy airy texture of this flour sets it apart from the very dense flour alternatives most commonly used in keto baking. Because of its close relation to the peanut, people with peanut allergies should likely steer clear! Read more about lupin flour here!

Almond flour and coconut flour are pretty commonly used in the keto baking world. I have tons of recipes where I use a blend of the two. I find that almond flour on its own is too dense and wet, and coconut flour is very drying. This cinnamon sugar muffin recipe uses a combination of these two flours, and my fathead pizza dough also uses both almond and coconut flour! While these recipes achieved a great texture and crumb using a carefully selected ratio of the two flour substitutes, adding lupin flour to the mix really elevated the game.

What is Vital Wheat Gluten? Vital wheat gluten is a flour-like powder that contains almost all glutenous protein and almost none of the starch of the wheat flour. Vital wheat gluten is made by first hydrating wheat flour, then processing it to remove everything except the gluten. The gluten is then dried out and ground into a fine powder. This finely ground powder can be added to keto and low-carb baked goods to help improve elasticity and create better crumb and chewiness. My flour blend uses 1/2 of a tablespoon of vital wheat gluten per cup and that only adds 0.5g of net carbs!

What is Oat Fiber? Oat fiber is ground from the husks of oats and it has zero calories and zero net carbs! Just a couple tablespoons of oat fiber can improve the texture and crumb of your keto baked goods and with zero net carbs, it’s a no-brainer! Oat fiber is a great source of fiber as its name suggests mixing it into smoothies, breadings, and other recipes can help you hit your daily fiber quota.

Xanthan gum is a binding agent commonly used to help improve the elasticity and stickiness in doughs and batters. Xanthan gum can also be used to thicken keto gravies and jams!

Erythritol is an organic compound called a sugar alcohol. Erythritol is naturally occurring and has a sweet flavor. When 1 gram of sugar alcohol is present in a cup of flour substitute, you can subtract 1 gram of net carbs. It is a very small amount and it does not affect the flavor of this flour blend. If you prefer not to use erythritol or if you have an allergy, then the carb count would be 1 gram higher, otherwise, it would not affect the functionality of the flour itself.

My Keto Lupin Flour Blend
This blend of flours produces the most bread-like texture, crumb, and chew of any low-carb flour substitute I have used to date!
5 from 7 votes
Prep Time 2 mins
Total Time 2 mins
Course pantry
Cuisine universal
Servings 1
Calories 458 kcal


  • measuring cups
  • measuring spoons


  • ¼ cup plus 2 tbsp of lupin flour
  • ¼ cup plus 2 tbsp of almond flour
  • 1 tsp coconut flour
  • 2 tsp oat fiber
  • ½ tbsp vital wheat gluten
  • ¼ tsp xanthan gum
  • ¼ tsp erythritol


  • Combine all ingredients in a container with a lid and whisk to make sure everything is distributed evenly. Store in a cool dry place for up to 6 months.


Nutrition Information for 1 cup of Lupin Flour Blend:
Calories: 458
Fat: 27.5g
NC: 5.1g 
Protein: 27g 
Keyword flour, flour blend, keto flour blend, low-carb flour blend

What To Buy To Make These Muffins

Lupin Flour

This light and fluffy flour alternative is low in carbs, and will elevate your keto baked goods!

Vital Wheat Gluten

Vital wheat gluten will help give structure and elasticity to your baked goods without adding all of the carbs found in wheat products.

Oat Fiber

Oat fiber improves the structure and texture of baked goods, and it adds zero net carbs!

I have used this flour blend to make chocolate chip cookies, zucchini muffins with cream cheese frosting, and these gorgeous pumpkin muffins so far, and all of them have turned out brilliantly! This flour blend is a little extra work, but I promise you the effort is WORTH IT! Just look!

Making The Pumpkin Muffins

When you are toasting your candied pecans, watch them carefully. I chopped them before toasting because I wanted the candied coating to be well distributed, but this does make them a little more susceptible to burning. I let them go for five minutes, stirred, and gave them another 2 minutes. They could have probably had a minute or more in the oven, but I played it safe!

I used a melon baller which I sprayed with pam to hollow out my muffin batter and create space for the cream cheese filling. It worked like a charm! To fill the muffins I used a Ziploc bag, and I cut one corner off. If you have a pastry bag (and your husband did not cut a giant hole in the end of it so it can only be used with the most giant of pastry tips and for no other earthly purpose 😒), then that would probably work just as well!

Pumpkin Muffins in Baking Tin
Keto Pumpkin Muffins with a Cream Cheese Filling Topped with Crunchy Candied Pecans
Pumpkin muffins cooling on a wire rack

Keto Pumpkin Muffins with a Cream Cheese Filling Topped with Crunchy Candied Pecans
These pumpkin muffins are spiced with cinnamon, nutmeg, ginger, and clove, with a creamy cheesecake-like center, and then topped with pecans that are candied with butter, cinnamon, and monk fruit sweetener. All of your favorite Fall flavors baked into a muffin!
5 from 7 votes
Prep Time 20 mins
Cook Time 30 mins
Total Time 50 mins
Course Breakfast, Dessert
Cuisine American
Servings 16
Calories 185 kcal


Candied Pecans

  • ½ cup pecans roughly chopped
  • 2 tbsp butter melted
  • 1/4 tsp cinnamon
  • 2-3 tsp granulated monk fruit sweetener

Pumpkin Muffin Batter

  • cups Lupin Flour Blend (*See recipe notes)
  • 1 tsp baking soda
  • ½ tsp salt
  • 2 tsp pumpkin spice (or more-you can measure with your heart)
  • ¾ cup unsweetened pumpkin puree
  • 2 whole eggs
  • ¼ cup butter melted
  • ¼ cup coconut oil melted
  • 1 cup granulated monk fruit sweetener
  • 2 tsp vanilla

Cream Cheese Filling

  • 4 oz cream cheese at room temperature
  • 1 whole egg
  • 2-3 tbsp granulated monk fruit sweetener
  • 1 tsp vanilla extract


Candied Pecans

  • Preheat the oven to 350°
  • Roughly chop 1/2 cup of pecans.
  • Melt two tablespoons of butter and toss the chopped pecans in the butter in a small mixing bowl. Add the monk fruit and cinnamon and toss again.
  • Spread the coated pecans evenly on a baking sheet. Bake for 5 minutes, stir, then bake for 2 or 3 more minutes. Watch them carefully so they don't burn.
  • Remove them from the baking tray and reserve them for later.

Pumpkin Muffin Batter

  • Preheat the oven to 375° and line a muffin tin with paper liners (plus 4 in another tin).
  • Combine the flour, baking soda, salt, and pumpkin spice in a mixing bowl.
  • Combine the butter and coconut oil and melt in the microwave.
  • In a separate mixing bowl combine the pumpkin puree, oil, butter, eggs, vanilla, and monk fruit.
  • Combine the wet and dry ingredients until incorporated. The batter will be thick. Distribute the batter evenly into 16 muffin cups.
  • spray the end of a small melon baller with pam spray, then use it to hollow out the center of each muffin.

Cream Cheese Filling

  • Combine the cream cheese, 1 egg, monk fruit, and vanilla to the bowl of a stand mixer. Mix on high speed until smooth.
  • Spoon the filling into a Ziploc or pastry bag. If you are using a Ziploc, then snip off one corner with a pair of scissors and pipe cream cheese filling into the center of each muffin.
  • Place the trays in the oven and bake for 20 minutes at 375°
  • Remove from the oven. Sprinkle candied pecans on top of each muffin, pressing them gently into the warm muffin tops so they adhere. Place back in the oven for two more minutes.


Nutrition Information for 1 Muffin: 
Calories: 185 
Fat: 16.7g
Net Carbs: 1.8g 
Protein: 5g 
*This recipe was developed using my lupin flour blend. It is totally worth it to check that recipe out in the above article, but if you prefer to use a more common blend of flours, then I would suggest using the following in place of the lupin blend: 
1 and 1/4 cup of almond flour 
1/4 cup of coconut flour 
1/2 tsp xanthan gum 
This will change the macros for the recipe slightly. 
Keyword keto breads, keto muffins, muffins

Let’s Eat!

If you tried this recipe and loved it, then head over to Facebook and tell me all about it! Check out more great content on Pinterest too!

These pumpkin muffins are just one of the many reasons to celebrate the coming Fall season. Goodbye, torturous heat, goodbye creepy bugs, back to school with my dear sweet children, and hello pumpkin muffins!

As always, happy snacking!

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