These easy Keto Pumpkin Bran Muffins have all the delicious flavor of the classic without the added carbs. Packed with pumpkin and spice, these sweet, tender muffins make fall mornings even more delightful.

My mum made the BEST bran muffins when I was growing up. Turns out that they were from a packaged mix, but I loved them nonetheless. They were dark brown, astonishingly tender, and very, VERY sweet. I never thought I could have such a thing on a keto diet! Until now…
Long ago, I created a low carb pumpkin “bran” muffin made with flax seed meal. It was good, but it had that slightly odd taste that comes along with using a lot of flax. However, I’ve found that pecan flour has a flavor very reminiscent of bran and I decided to test that out. It’s a fabulous replacement for bran in a keto muffin recipe!

Why It Works
Bran is the tough outer layer of whole grains that is removed during the milling process. Most recipes use wheat bran, but there is also oat bran, rice bran, and other varieties. All of which are too high carb for the keto diet.
Both pecan flour and flax seed meal have a texture and flavor reminiscent of wheat bran. Unlike almonds, pecans are difficult to blanch so the “flour” usually contains a lot of the skin. This makes it more coarse and dry in keto baked goods. The sweet nuttiness of pecan flour also adds a unique depth of flavor.
Ingredients and Substitutions
- Almond flour: This is the base flour for these muffins. I don’t recommend using all pecan flour (or flax meal) as it will make them very dry and not nearly as tasty.
- Pecan flour: I recommend purchasing the pecan flour (aka pecan meal) as it will be more finely ground than anything you can do at home. You can swap it out for ground flax seed in the same amount.
- Sweetener: A brown sugar replacement offers the best flavor for these muffins. Please see the Sweetener Options section for more information.
- Protein powder: You can use whey protein, egg white protein, and plant-based protein. Do not use collagen or bone broth protein.
- Pumpkin pie spice: You can also make your own mix with a combination of cinnamon, ginger, and cloves or nutmeg.
- Pumpkin puree: A thicker, canned puree works best.
- Baking Staples: Butter, eggs, baking powder, salt, vanilla extract.
- Optional: Shelled pumpkin seeds (pepitas) or chocolate chips.
How to Make Keto Pumpkin Bran Muffins

- Combine the dry ingredients: In a large bowl, whisk together the almond flour, pecan flour, sweetener, protein powder, pumpkin pie spice, backing powder, and salt.
- Add the wet ingredients: Stir in the pumpkin, eggs, butter, and vanilla extract. Then stir in just enough water until you have a scoopable consistency.
- Fill the muffin cups: Divide the mixture evenly among 12 muffin cups lined with parchment or silicone liners. Sprinkle the tops with shelled pumpkin seeds, if desired.
- Bake: Bake the muffins until risen and just firm to the touch. Remove and let cool completely.


Carolyn’s Tips for Success
Protein powder is a necessary ingredient for these keto pumpkin bran muffins, as it helps them rise and be more fluffy. You can skip it if you must but please be aware that it will affect the texture.
If you make your own pumpkin puree, it’s likely thinner than the canned variety. You will probably need less water for the batter, so hold back until you see the consistency.
Parchment or silicone liners are a must. Paper liners will stick to the muffins like crazy!
Sweetener Options
Classic bran muffins take brown sugar and often some molasses. So a brown sugar replacement is the next best option for keto. I generally recommend using an erythritol based sweetener for muffins because allulose can brown very quickly.
You are free to use whatever you like best but you need to understand how it will affect the outcome. I suggest reading my Comprehensive Guide to Keto Sweeteners.

More Pecan Flour Recipes To Love

Keto Pumpkin Bran Muffins
Ingredients
- 1 1/2 cups (168 g) almond flour
- 1 cup (99 g) pecan flour, (or flax seed meal)
- 1/2 cup (100 g) brown sugar replacement
- 1/3 cup (36 g) whey protein powder
- 2 1/2 tsp baking powder
- 2 tsp pumpkin pie spice
- 1/4 tsp salt
- 3/4 cup (183.75 g) pumpkin puree
- 3 large eggs, room temperature
- 1/3 cup (75.67 g) butter, melted
- 1 tsp vanilla extract
- 3 to 5 tbsp (45.65 g) water
- 1/4 cup (25 g) pepitas (shelled pumpkin seeds), optional
Instructions
- Preheat the oven to 350ºF and line a standard muffin tin with silicone or parchment muffin liners.
- In a large bowl, whisk together the almond flour, pecan flour, sweetener, protein powder, baking powder, pumpkin pie spice, and salt.
- Add the pumpkin puree, eggs, butter, and vanilla and stir until well combined. Stir in just enough water until the mixture is easily scooped (it should not be pourable).
- Divide the mixture between the prepared muffin cups and smooth the tops. Add a few pepitas to the top of each muffin and press lightly to adhere.
- Bake 25 to 30 minutes, until the muffins have risen and are just firm to the touch on top. Remove and let cool completely in the pan.
Notes
Nutrition
Nutritional Disclaimer
Please note that I am not a medical or nutritional professional. I am simply recounting and sharing my own experiences on this blog. Nothing I express here should be taken as medical advice and you should consult with your doctor before starting any diet or exercise program. I provide nutritional information for my recipes simply as a courtesy to my readers. It is calculated using MacGourmet software and I remove erythritol from the final carb count and net carb count, as it does not affect my own blood glucose levels. I do my best to be as accurate as possible but you should independently calculate nutritional information on your own before relying on them. I expressly disclaim any and all liability of any kind with respect to any act or omission wholly or in part in reliance on anything contained in this website.
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oh I just love pumpkin and these look wonderful
I just made these and they taste wonderful! The only problem I had was that they were a little “wet” even after cooking them an extra ten minutes. I think it was because I had too much liquid in my pumpkin puree. I had it in the freezer from last year and didn’t get all of the liquid out. I can’t wait to make the next batch and see if they turn out even better! I put some cream cheese and sprinkled erythritol on it. YUMMO!
Hmmm, good point about the pumpkin puree. Mine was canned and very thick, so I think pushing out more liquid would help. They are definitely on the moist side because of the pumpkin, but they shouldn’t feel wet. I may change the recipe to make a note of that. Thanks!
I am also having this issue of the wetness in the center that I can’t quite cook out without overcooking them. I was also using canned pumpkin, so I’m not sure why. I tried reducing the amount of wet ingredients and still had this issue. Considering adding a little coconut flour next time to help absorb it.
Do you have any suggestions? Can I omit the nutmilk completely or is it necessary for the rising?
Made these today and these are soooo yummy. I almost made 1/2 recipe of your delicious cream cheese frosting and put on top!
Thanks for all of your great recipes!
P.S. Also made your peanut butter cups today as well….almost very good!
LOL Interesting story!
I was wondering this about the Stevia? Do you know epwhy some recipes call for both Swerve and Stevia extract? I am still trying to understand the Swerve, splenda , stevia, ez-sweetz…. We have been using Ez sweetz drops (really tastes good and splenda with fiber. What are your thoughts?
Why both stevia and Swerve…because I like the combo. Because I personally think that they work well together to sweeten things. Also because I do understand that erythritol based sweeteners can be expensive. A bottle of stevia is expensive but it goes a loooooooong way. So for readers who don’t want to blow through their erythritol quickly, I think stretching it out with stevia can help.
Personally, I don’t like sucralose and splenda. I don’t like the way they taste. So I steer clear.
Hope that helps!
Oh I am sooo ready for these! Yaaaay for pumpkin muffins and pumpkin growers! 🙂
Yummy….these would go so perfect with the pumpkin spice coffee I’m drinking right now. Bring some over, will ya? 😉
I’ve seen alot of pumpkin recipes posted this week. Everyone must be looking forward to fall.. ( not me, I’m a summer person) .
I live in Bucks County , Pa and we have pumpkins growing on local farms, in our backyards , etc. They grow great here! Looks like a good recipe
I love the idea of using flaxseed meal instead of bran to make these muffins super healthy (and GF)! And it’s starting to be that pumpkin time of year again, so I’m enjoying anything and everything that includes this orange gem 🙂
These have my name written all over them! I am so excited about pumpkin season and can’t wait to pick up a few little ones to have in the apartment:-)
i could so use one of these right now
Oh, this one is a keeper, although it’s getting difficult to find unflavored whey protein powder around here. Will have to check out Amazon for it, although do you think vanilla might work? This is a perfect welcome-to-Fall recipe, IMHO. Thanks!
I adore bran muffins. My mom used to make them all the time. Totally love them.
another one I printed immediately after reading your commentary! Can’t wait to try and might just have to stock up on pumpkin.
The Matcha Frozen Yogurt Pops were FANTASTIC…and I’ll be doubling the recipe here on out…my DH looked at me eating the last one and said, “you’re going to eat the last one?”
I absolutely enjoyed it.
Yay for pumpkin recipes! I’m generally not a fan of bran muffins, but with the addition of pumpkin, I am totally on board.
this recipe is awesome…I can’t wait to try them!