Pumpkin Cream Cheese Muffins (gluten-free, whole grain, all-purpose options)

These pumpkin cream cheese muffins have a generous amount of filling and a streusel topping! Can be made with gluten-free, whole wheat or all-purpose flours. Thanks to Bob’s Red Mill for making today’s post possible!

These are some seriously moist pumpkin muffins. They’re probably more cupcake than muffin. If you want them more hearty and muffin-like and less fluffy, you can use half applesauce / half oil in place of all the oil. I’ve tried it but much prefer the all oil version.

And the cream cheese filling makes them so ridiculously delicious! Unlike some cream cheese or cheesecake goodies that really need to firm up or chill before serving, these are awesome straight from the oven.

You could skip the streusel if you’re short on time, but not the filling. ;) Unless you’re dairy-free and just want a yummy pumpkin muffin or cupcake recipe! For dairy-free, you’d also need to omit the streusel.

My pumpkin cupcakes are also a delicious option! They’re probably my favorite cupcake recipe ever. And for the streusel lovers, check out my pumpkin pie bars, which have a streusel crust and topping!

Pumpkin Cream Cheese Muffins – incredibly moist with a generous amount of filling! With gluten-free, whole grain and all-purpose flour options.

If you’re grain-free, you can try using the batter I used in my paleo pumpkin donut holes but I haven’t tried it in combination with the filling in these pumpkin cream cheese muffins. If you try it out, I’d love to hear how it goes! If you aren’t grain-free, you’ve got three different flour options for this recipe.

Up until maybe 1 1/2 years ago, my recipes were either whole wheat or gluten-free. But not both. But then I got a lot of requests for gluten-free versions of the whole wheat recipes, which led me to Bob’s Red Mill Gluten-free 1-to-1 Baking Flour, which you use cup for cup in place of all-purpose flour. You don’t have to add a thing! It really couldn’t be any easier.

I had tried some of the gluten-free flour blends here in Germany and thought they were pretty awful. Having flour shipped to Germany isn’t cheap so I read loads of reviews before deciding on this one.

Pumpkin Cream Cheese Muffins – super moist with a generous amount of filling! With gluten-free, whole grain and all-purpose flour options.

People wrote that this was the best gluten-free baking blend that they had ever used and some people even claimed that recipes sometimes come out better with this flour than with wheat flour. That was hard for me to believe so I had to give it a try.

And they were right. I think the gluten-free version of these pumpkin cream cheese muffins is actually a tiny bit better than the whole wheat version. They were moister. But that doesn’t mean you shouldn’t make the whole wheat version if you can have gluten! They’re still amazingly moist and delicious. :) And to be honest, my taste testers didn’t even notice a difference between the three types of muffins (all-purpose / gluten-free / whole wheat).

I’ve used this gluten-free 1-to-1 baking flour in so, so many recipes and only had it not work with a few. One was a yeasted donut recipe and they came out a little too dense. Another was a cookie recipe. That one still puzzles me but I couldn’t get any gluten-free flours to work well in either of those recipes. I think some recipes are just impossible to convert to gluten-free without making other adjustments to the recipe (like with the amount of fat, liquid, etc.)

Pumpkin Cream Cheese Muffins – amazingly moist with a generous amount of filling! With gluten-free, whole grain and all-purpose flour options.

And I’ve used it in some tart crust recipes, where the crust came out a bit more fragile than the all-purpose flour version. But I think that’s to be expected. If you want to make a gluten-free pie or tart crust, I recommend finding one that’s already gluten-free. Same with yeasted donuts! Those items can be finicky.

By the way, Bob’s Red Mill has a gluten-free pie crust mix and it’s awesome. I’ll be sharing a recipe with that soonish!

So it might not work 100% of the time in every recipe ever, but things usually come out just like they’re made with all-purpose flour. Not gritty, starchy, chalky or rubbery like some other mixes I’ve tried. This post is sponsored by Bob’s Red Mill but I had been using this flour long before we started working together. :) I hope you’ll try it out!

If you prefer a loaf version, check out this healthy pumpkin bread! Or want a low-carb version? Try these low-carb pumpkin cream cheese muffins!

Some other recipes I’ve made with it!

  • Key Lime Bars (gluten-free, whole grain, all-purpose options)
  • The Best Chocolate Cupcakes Ever! With gluten-free, whole wheat and all-purpose flour options.
  • Pumpkin Bourbon Bundt Cake with gluten-free, whole wheat and all-purpose flour options.

As always, all opinions expressed are my own. Head over to the Bob’s Red Mill coupon section for some $1 and $3 coupons! They’ve also got a lot of recipes using the gluten-free 1-to-1 baking flour on the product page (you have to scroll down about half-way and click on “Recipes”). I know I’ll definitely be trying these gingerbread cupcakes soon!

Pumpkin Cream Cheese Muffins (gluten-free, whole grain, all-purpose options)

Rated 5.0 by 2 readers
Pumpkin Cream Cheese Muffins (gluten-free, whole grain, all-purpose options)
  • Prep Time:
  • Cook Time:
  • Ready in:
  • Yield: 20 muffins


    For the cream cheese filling:

  • 12 ounces (340 grams) cream cheese1
  • 6 tablespoons raw sugar or granulated sugar
  • 1 teaspoon vanilla extract
  • pinch of salt
  • For the streusel:

  • 1/4 cup (50 grams) brown sugar or raw sugar
  • 1/4 cup (50 grams) granulated sugar or raw sugar
  • 1 teaspoon ground cinnamon
  • 1/4 cup (34 grams) Bob's Red Mill Gluten-free 1-to-1 Baking Flour or 1/4 cup (31 grams) whole wheat flour, white whole wheat flour or all-purpose flour
  • 1/8 teaspoon salt
  • 3 tablespoons (42 grams) unsalted butter
  • For the batter:

  • 2 cups (268 grams) Bob's Red Mill 1-to-1 gluten-free baking flour or 2 cups (250 grams) whole wheat flour, white whole wheat flour or all-purpose flour
  • 1 1/2 teaspoons baking soda
  • 3/4 teaspoon baking powder
  • 1 1/2 teaspoons ground cinnamon
  • 1 teaspoon ground ginger
  • 1 teaspoon ground nutmeg
  • 1/2 teaspoon ground cloves
  • 1/2 teaspoon salt
  • 2 large eggs (50 grams each, out of shell), room temperature
  • 1 cup (200 grams) brown sugar or raw sugar
  • 1/2 cup (100 grams) granulated sugar or raw sugar
  • 1/4 cup (60 milliliters) maple syrup
  • 3/4 cup (177 milliliters) olive oil2 (or another neutral-tasting oil that's liquid at room temp)
  • 1 15-ounce (425-gram) can pumpkin puree


  1. Preheat the oven to 325°F (163°C). Line two cupcake pans with 20 paper liners.
  2. Prepare the filling. In a medium bowl using an electric hand mixer, beat all filling ingredients at medium speed until light and fluffy. Set aside.
  3. Prepare the streusel. In a small mixing bowl, stir together the sugars, cinnamon, flour and salt until combined. Use your fingers to add in the butter until well combined. Set aside.
  4. Prepare the batter. In a large mixing bowl, mix together the dry ingredients (flour through salt). In another large bowl , mix together the eggs, and then add the rest of the ingredients (sugars through pumpkin puree). Stir until combined. Add the dry mixture to the wet mixture and mix just until combined (do not over mix!).
  5. Pour about 1 tablespoon of batter in each liner. Then add 4 teaspoons of filling (try to keep the filling in the middle of the muffin and not spread all over). Top with about 3 tablespoons of batter and 1 1/2 teaspoons (9 grams) of the streusel.
  6. Bake for 21-23 minutes or until a toothpick inserted in the side comes out clean (being careful not to confuse raw batter with cream cheese filling). Remove from the oven and let the cupcakes cool in the pan for 10 minutes and then very carefully remove them to a wire rack to cool completely, about 1 hour. Store at room temperature in an airtight container for 1 day or refrigerate for up to 4 days.


  1. If you live outside of North America and have the kind of cream cheese that's meant for toast (that comes in a little plastic tub) rather than American style brick cream cheese, then get a 450 grams of cream cheese, place it in the center of a cheesecloth, and wring out the liquid until you have 340 grams of cream cheese left.
  2. If you use olive oil, the batter will taste like olive oil but the taste disappears after baking.

Recipe by  | www.texanerin.com

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57 comments on “Pumpkin Cream Cheese Muffins (gluten-free, whole grain, all-purpose options)” — Add one!

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  • Michelle says
    October 21, 2016 @ 7:34 am

    Excellent recipe- I made both wheat and gluten free versions to rave reviews. For Canadian readers, I use Bulk Barn’s 1:1 gluten free flour mix (in place of Erin’s suggested Bob’s Red Mills) and the muffins come out beautifully with an extra 3-4 minutes of baking time. The streusel topping also works very well with almond flour.

    • Erin replies to Michelle
      October 21, 2016 @ 9:26 pm

      I love that you made both versions! Thanks for the tip for the Canadian readers. :) That’s interesting that almond flour worked in the topping! Did you use the same amount? Thanks so much for your feedback!

  • Jeanna B says
    October 18, 2016 @ 4:25 pm

    This batter also bakes well in a loaf pan! I used a pan that makes 4 mini loafs and baked them for 35-40 minutes at 325 degrees F. I used the pumpkin batter and then topped with the streusel. It is so moist that it is a crossover between a pumpkin bread and a pumpkin cake. So good!

    • Erin replies to Jeanna B
      October 18, 2016 @ 5:37 pm

      Oooh! That’s great to know. So did you not include the cream cheese filling? Thanks so much for including the pan sizes and baking time + temperature! :) I’ll have to try that out. I’m happy you enjoyed the recipe and thanks for your comment!

      • Jeanna B replies to Erin
        October 18, 2016 @ 8:55 pm

        Nope, I didn’t use the cream cheese filling for the bread. I made a dozen of the muffins with all three parts, but then ran out of cream cheese filling and had a ton of batter left over because I’m bad at portioning (haha!). So, instead of wasting the rest of the batter I decided to try baking it as a loaf and it worked! Yay!! :) thanks for the recipe!

        • Erin replies to Jeanna B
          October 20, 2016 @ 1:45 pm

          Haha. I’m bad at portioning, too. ;) And that’s some great info. Thanks again for your feedback!

  • Lora @savoringitaly says
    October 18, 2016 @ 12:41 pm

    The one thing I haven’t baked in pumpkin season is muffins and now I have to bake these! Good to know about the Bob’s Red Mill GF flour…I am experimenting sometimes with things for when my GF friends come to eat with us. These look fabulous!

    • Erin replies to Lora @savoringitaly
      October 18, 2016 @ 5:39 pm

      You HAVE to try their flour! It makes GF baking so very easy. I hope you’ll enjoy the muffins! :)

  • Connie Ehresman says
    October 18, 2016 @ 8:32 am

    Hi! I don’t know if you’ve been asked this yet, but do you share anything Paleo? Can I substitute the flour in these with coconut or almond flour? Thanks!
    I hope I don’t miss your reply. I am disabled and don’t check my fb or tablet (email) as often as I should!

    • Erin replies to Connie Ehresman
      October 18, 2016 @ 8:36 am

      Hello! I have lots of paleo recipes. :) You can see them here: paleo recipes. The cream cheese and regular / brown sugar in these muffins (along with the flour, which isn’t interchangeable with paleo flours) isn’t paleo, but I mention a grain-free version possibility after the first picture in the post. I hope that helps! :)

  • Kim Beaulieu says
    October 17, 2016 @ 12:31 am

    Erin, do you know if they carry this particular flour in Canada? I’d love to try it. If not I can pick some up next time we travel to the states.

    • Erin replies to Kim Beaulieu
      October 18, 2016 @ 5:58 pm

      I found a Canadian site that sells BRM but didn’t see that flour there. But I know you go to the US often so you should easily be able to find it there. :) I know you’ll love it!

  • Lisa @ Wine & Glue says
    October 16, 2016 @ 11:25 pm

    This has pretty much everything I want in a muffin! Yummy!

  • Michelle says
    October 16, 2016 @ 11:13 pm

    Wow. I made these yesterday (gluten free) and they were amazing! I am so glad I found your website.

    • Erin replies to Michelle
      October 18, 2016 @ 5:59 pm

      Yay! I’m so very happy to hear that. :) I’m happy you found my website, too! Thanks for taking the time to leave feedback.

  • Angie | Big Bear's Wife says
    October 13, 2016 @ 5:06 pm

    skip the streusel………haha never skip the streusel! lol I Really would love these either way!

  • Liz says
    October 13, 2016 @ 11:21 am

    These rock my world!!! We love pumpkin bread and muffins around here and you just kicked them up a whole bunch of notches!!!

    • Erin replies to Liz
      October 18, 2016 @ 6:02 pm

      Aww, thanks! :)

  • Cookin Canuck says
    October 13, 2016 @ 6:22 am

    That cream cheese filling looks perfectly gooey and decadent. I have a feeling I wouldn’t be able to stop at just one of these beauties.

  • Lauren says
    October 13, 2016 @ 4:37 am

    I love how many options there are with these! Although skipping the streusel is never an option in my opinion. ;)

    • Erin replies to Lauren
      October 18, 2016 @ 6:02 pm

      Haha. So many comments on omitting the streusel! I’m sorry, y’all. ;)

  • Ashley @ Wishes & Dishes says
    October 13, 2016 @ 1:26 am

    That filling…and that streusel! No way would I skip it! These look perfect.

  • Joanie @ ZagLeft says
    October 12, 2016 @ 11:55 pm

    These look fantastic. A muffin in the morning with coffee is my favorite way to start the day. Plus, the bit of cream cheese makes them even more perfect.

    • Erin replies to Joanie @ ZagLeft
      October 18, 2016 @ 6:03 pm

      The cream cheese makes them soooo ridiculously delicious!

  • Catalina @ Peas & Peonies
    October 12, 2016 @ 7:39 pm

    Yummy! It looks really delicious! And I adore muffins so I will try it for sure!

  • Brandy | Nutmeg Nanny says
    October 12, 2016 @ 7:03 pm

    That streusel topping! Looks delicious! These would totally be dangerous i my house!

  • Cathy | Lemon Tree Dwelling says
    October 12, 2016 @ 6:38 pm

    I wouldn’t dream of skipping the filling OR the streusel…these muffins look perfect!

  • Kim Beaulieu says
    October 12, 2016 @ 7:14 am

    These look amazing. Nothing beats a great muffin in the morning. Love the cream cheese in there too. Yum!

  • Sandi Gaertner says
    October 12, 2016 @ 7:09 am

    Now this is my kind of muffin! Bring on the fall flavors!

    • Erin replies to Sandi Gaertner
      October 18, 2016 @ 6:06 pm

      All time, all the time. At least until the day after Thanksgiving. ;)

  • Mary says
    October 12, 2016 @ 4:29 am

    Haven’t made these yet, but I did find a typo.

    In the ingredient list you have: 1/4 cup (34 tablespoons) Bob’s Red Mill Gluten-free 1-to-1 Baking Flour.

    I’m pretty sure that it should be 4 tablespoons. Unless of course, my math is really off. :-)

    • Erin replies to Mary
      October 12, 2016 @ 1:25 pm

      Oh my goodness! Thanks for catching that. It was supposed to say grams. Fixed it! Thanks again and I hope you’ll get the chance to try these out. :)

      • Diane replies to Erin
        October 14, 2016 @ 12:55 am

        ?? It isn’t fixed – I just noticed it, too.

        • Erin replies to Diane
          October 14, 2016 @ 9:10 am

          So strange! It seems to have stuck this time. Thanks for your comment!

  • Kirsten/ComfortablyDomestic says
    October 12, 2016 @ 4:23 am

    I’m loving the cream cheese filling!

  • Kimberly @ The Daring Gourmet says
    October 12, 2016 @ 4:18 am

    Yummy, it’s always that cream cheese filling that gets me, my favorite part! :)

  • The Food Hunter says
    October 12, 2016 @ 12:24 am

    I thought I was over the pumpkin thing…until I saw this.

    • Erin replies to The Food Hunter
      October 18, 2016 @ 6:08 pm

      Whaaat?! It’s only my second pumpkin post of the year! Don’t be sick of it quite yet! ;)

  • Brenda @ a farmgirl's dabbles says
    October 11, 2016 @ 11:35 pm

    That streusel looks WONDERFUL on top! Beautiful muffins!

  • Karyn Granrud says
    October 11, 2016 @ 8:16 pm

    GF mixes confuse me all the time. I wish I had better luck baking with GF flour. These muffins look AMAZING!! Pinned them for ya!

    • Erin replies to Karyn Granrud
      October 18, 2016 @ 6:08 pm

      You have to try this one! You use it 1 to 1 in place of AP flour. Couldn’t be any easier!

  • Lauren Kelly Nutrition says
    October 11, 2016 @ 8:03 pm

    I’m not skipping the filling or the streusel! These look incredible, Erin!

  • Amy @ Little Dairy on the Prairie says
    October 11, 2016 @ 6:51 pm

    I can’t decide what I like most about this muffin, the spicy pumpkin muffin, the creamy center, or that topping! I think I just want the whole thing!

  • Kelly Barcroft
    October 11, 2016 @ 5:36 pm

    Those really tasty! I’ll probably try out in the near future. I know a lot of people traveling and I can make these as a snack for them and try one our myself…that way I don’t eat them all myself. I know you understand that!

    • Erin replies to Kelly Barcroft
      October 12, 2016 @ 1:28 pm

      Thanks! When I tasted them straight out of the oven to see how what the filling was like, I might have eaten 4. :/ So I think that plan of yours is very smart! I hope everyone will enjoy them. :)


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