Whole Wheat Pumpkin Muffins

These Whole Wheat Pumpkin Muffins are lower in sugar than most recipes and filled with whole grains!

Well, friends…it’s fall. The weather’s getting cooler, the days are getting shorter and I opened my first can of pumpkin.

Unfortunately, (or fortunately?), it was a jumbo can. Fortunately, I’m still on vacation…so that means I had time for recipe testing! Over the past week I’ve been working hard on a recipe for pumpkin muffins. I knew I wanted them to be healthy and after looking at a bunch of recipes online, I wasn’t crazy about the amount of sugar that was in most of the recipes.

These Whole Wheat Pumpkin Muffins are lower in sugar than most recipes and filled with whole grains!

So, I set to work adding, subtracting and rearranging to make my own! Here are some of the recipes I used for inspiration:
Whole Wheat Pumpkin Muffins
Spiced Pumpkin Honey Muffins
Oat Flour Pumpkin Bread
Fat-Free Pumpkin Bread
Wheat-free, Dairy-free Pumpkin Bread

They all sound good…they just weren’t what I was looking for. I decided I wanted to totally eliminate brown and white sugar from the recipe, which I’d never done before. My plan was to replace it with natural sweeteners like brown rice syrup and honey.  After I’d worked out my recipe, I did a trial run. I quartered the recipe I came up with so it only made 4 muffins in case it went horribly wrong.

Trial #1
They were good enough to eat, but definitely too moist in the middle. I decided I needed to add more dry ingredients so I thought I’d try it with oats. But sometimes I’m not crazy about whole oats in my muffins, so I ground them up to make oat flour. I also reduced the amount of applesauce a little bit.

Trial #2
Better! They definitely weren’t as wet in the middle. The oat flour gave them a little bit of texture but nothing extreme, and the flavor was good.

Trial #3
I was pretty much satisfied with the recipe so after one more tweak (reducing the amount of applesauce again), I finalized the recipe. Then I halved it and made my final trial run. I thought it would make six muffins since my trial runs, where I quartered the recipe had been making four, but it ended up making 8 large muffins. It could easily have made 10-12 smaller muffins so that’s the one I’ve listed below.

Whole Wheat Pumpkin Muffins

by Lindsay L

Prep Time: 5 min

Cook Time: 25 min

Keywords: bake breakfast muffins snack vegetarian healthy pumpkin fall summer winter

Ingredients (8-12 muffins)

  • ½ c pumpkin
  • 1 egg
  • 2 Tbsp applesauce
  • ¼ c brown rice syrup
  • ¼ c honey
  • ½ tsp vanilla
  • 1 c white whole wheat flour
  • ¼ c oat flour
  • ¼ tsp salt
  • 1 tsp cinnamon
  • ¼ tsp ginger
  • ¼ tsp nutmeg
  • ½ tsp baking soda
  • ½ tsp baking powder


1. Combine the wet ingredients in a bowl.

2. Add the dry ingredients and stir until just combined.

3. Spoon into greased or lined muffin tins and bake at 350 degrees F for 20-25 minutes.


Let cool completely before trying to remove muffin liners or they will stick.

Spice quantities can be increased or decreased based on preference.

You could also substitute pumpkin pie spice if you have it.

If you don’t have oats to make oat flour, you can use all wheat flour.

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These Whole Wheat Pumpkin Muffins are lower in sugar than most recipes and filled with whole grains!These Whole Wheat Pumpkin Muffins are lower in sugar than most recipes and filled with whole grains!
And just for fun, here’s one I snapped with my phone…pretty good, eh?

These Whole Wheat Pumpkin Muffins are lower in sugar than most recipes and filled with whole grains!
And a fun filter:

These Whole Wheat Pumpkin Muffins are lower in sugar than most recipes and filled with whole grains!

Happy Friday! Have a great weekend :)


About Lindsay

Lindsay Livingston is a Registered Dietitian and new mom from Columbus, Ohio. On her blog, she shares simple, healthy recipes, nutrition tips, workouts and snapshots of her life. Follow her on Twitter @LeanGrnBeanBlog and Instagram @TheLeanGreenBean and be sure to subscribe via RSS or email so you never miss a post!


  1. lindsay, the photos on this post are awesome! nice work, girl! :) oh yeah, and the muffins look pretty delish too…!
    sarah (sarah learns) recently posted..fondue for two

  2. And yes, that confirms it…I DO need to start stocking up on pumpkin. :)
    Sarah @ The Smart Kitchen recently posted..Dive! [A Film About Food Waste In America]

  3. sounds good! i made pumpkin muffins this week too :)
    Sarah K. @ The Pajama Chef recently posted..Corn Cake Salad

  4. Okay i just opened a huge tin of pumpkin so i HAVE to make these!
    Looks delish!!!
    Whats the filter you used on that photo, its great!
    Donna @ Life of a Happy Blonde recently posted..So Long, Farewell

  5. How fun! I’ve yet to open my first can, I’m waiting for the perfect application. I want to be on vacation so I can experiment all I want with my pumpkin stash!
    Kaitlyn@TheTieDyeFiles recently posted..Gone Bananas

  6. yum pumpkin muffins, we made a batch of our first pumpkin muffins of the season a few weeks ago, and boy did they hit the spot! excited for pumpkin season!!
    Pure2raw Twins recently posted..creamy cashew cream

  7. It’s so cool that you kept experimenting until getting it just right! That’s dedication. As a person who is intimidated by baking and the science of it, I have to say I’m impressed. And I like the photo with the filter–very funky looking!
    Jenna recently posted..Putting the ‘everything’ in ‘Everything’

  8. Pumpkin is so on everyone’s mind today – including mine! I’m going to make pumpkin risotto tonight and pumpkin pancakes tomorrow!
    LauraJayne recently posted..Classifieds

  9. I very much love pumpkin ANYTHING especially muffins! I keep forgetting to buy pumpkin at the store- doh!

    I’m thinking of doing pumpkin spice cupcakes soon! :)

    Happy Fall- although it’s 90 here!
    Carissa recently posted..Feels Like Home

  10. those do look tasty.

    a question just because i’m curious – why do you think that rice syrup and honey are so much better than brown sugar? not that they aren’t – i really don’t know and that is why i’m asking. and by the way – where does one get rice syrup?

    • hi jacquie! brown rice syrup, honey and agave are complex sugars which means they have a lower glycemic indexes than sugar and they don’t make your blood sugar spike and fall as quickly as white sugar. it order my brown rice syrup online from swanson health products. you can usually find a coupon code for free shipping so it’s pretty cheap!

  11. Wow – I am impressed with your determination to get the perfect muffin! I already planned to break out the pumpkin tomorrow too – starting with a pumpkin shake for breakfast :-)
    Diana @ VeggieNextDoor recently posted..Visiting Home & Mom’s Kitchen Sink Stir-fry

  12. I have to say you have inspired me. I’ve only been following you for a few months and learning so much! These muffins are exactly what I need/love for a cool and wet west coast morning! I may even share them with my kiddies!

    I’m a newbie to the healther side of baking and haven’t really experimented outside of applesauce! My brand new bottle of Agave Syrup (raw) has been sitting in my pantry waiting for the best usage. If I were to use this instead of the brown rice syrup would it be 1:1?
    Can’t wait to see what else your “comfort” food is! :)

  13. I think I’m the only blogger that doesn’t care for pumpkin!
    Matt @ The Athlete’s Plate recently posted..To Thine Own Self Be True

  14. Oh yum yum yum, so happy I found your blog, these look fantastic! Pictures are great but I best the taste was incredible. And pumpkin too, you’ve got to love the fall.
    Laura @ A Healthy Jalapeño


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