We’ve had a slight chill in the air for a few consecutive days now, which has me finally experiencing those old familiar yearnings for fall.  Like so many of you, baking with fall flavors and spices is way high up on the list of reasons I love this season so.  Every year when the time finally arrives, it is such fun to bake that favorite inaugural treat, whatever your favorite may be.  In our home, the pumpkin cream cheese muffins I have been making for years will forever hold the number one spot.

The original version, while irresistibly delicious, tend more toward dessert than legit breakfast food.  However, Andrew adores these muffins and asks for them all the time.  Last fall and winter, we kept them in near constant supply in the freezer to pull out for his breakfast many days.  As soon as I realized they were becoming more routine than special treat, I gave them a mini-makeover to make them more suitable breakfast food.  We’ve been making them this way for a while, so I figured it was high time I shared the lightened up version with you.  The all-purpose flour is replaced by white whole wheat, much of the oil is replaced by applesauce, and the sugar is reduced.  I added oats to the streusel topping for extra texture and a bit of fiber.  These are still a hit with our whole family but now we feel much better about eating them.


For the filling: 
8 oz. cream cheese (reduced fat is fine), at room temperature
2 tbsp. honey

For the muffins: 
3 cups white whole wheat flour
1 tsp. ground cinnamon
1 tsp. ground nutmeg
½ tsp. ground cloves
1 tbsp. plus 1 tsp. pumpkin pie spice
1 tsp. salt
1 tsp. baking soda
4 large eggs
1½ cups sugar
2 cups pumpkin puree
½ cup vegetable or canola oil
¾ cup unsweetened applesauce

For the topping:* 
4 tbsp. white whole wheat flour
7 tbsp. old fashioned rolled oats
3 tbsp. turbinado (coarse) sugar
½ tsp. ground cinnamon
3 tbsp. cold butter, cut into pieces


  • 01

    To make the filling, combine the cream cheese and honey in a bowl.  Beat with an electric mixer until smooth.  Transfer to a pastry bag.  Pipe into 24 equal dollops onto a parchment-covered baking sheet.  Freeze until firm, at least 3 hours or overnight.

  • 02

    To make the muffins, preheat the oven to 350˚ F. Line muffin pans with paper liners. In a medium bowl, combine the flour, cinnamon, nutmeg, cloves, pumpkin pie spice, salt and baking soda; whisk to blend. In the bowl of an electric mixer combine the eggs, sugar, pumpkin puree, oil and applesauce. Mix on medium-low speed until blended. With the mixer on low speed, add in the dry ingredients, mixing just until incorporated.

  • 03

    To make the topping, combine the flour, oats, sugar, and cinnamon in a small bowl; whisk to blend. Add in the butter pieces and cut into the dry ingredients with a pastry blender or two forks until the mixture is coarse and crumbly. Transfer to the refrigerator until ready to use.

  • 04

    To assemble the muffins, fill each muffin well with a small amount of batter, just enough to cover the bottom of the liner (1-2 tablespoons).  Place a dollop of the cream cheese mixture into each muffin well. Divide the remaining batter among the muffin cups, placing on top of the cream cheese to cover completely. Sprinkle a small amount of the topping mixture over each of the muffin wells.

  • 05

    Bake for 20-25 minutes. Transfer to a wire rack and let cool completely before serving. (It may be hard to resist immediate consumption, but the cream cheese filling gets very hot!)

  • 06

    *Topping is completely optional, and they are good both ways.  I think some chopped pecans or walnuts would also be very good mixed in with the topping.


  • Erin Chewning

    The original recipe for these muffins have been a favorite of mine since I tried them last year. Can’t wait to give the lighter version a try!

  • HalfBakedHarvest

    These look so perfect! Bring on fall and cozy baking weather!

  • Ruth

    These look great, Annie! Thank you for making the recipe healthier. Like Andrew, I love my muffins so healthifying is a MUST. I have had great results using similar modifications with my other muffin recipes and I am betting these will be great as well. Thanks, again.

  • Christina

    I was going to make pumpkin muffins this weekend but didn’t have time. I’ll be saving this one for later!

  • The original ones have made me a tiny bit famous at my daughter’s school :) I’ll totally give these a try! Can’t wait!

  • Jealous of your cooler weather! And I love how you adapted these muffins to make them lighter.

  • Liz N.

    Pumpkin in back in my household too. Thank you for lightening up this recipe. I also love that you pre-portioned out the cream cheese filling for ease of filling! Brilliant! I’m making your recipe for Pumpkin Spice Syrup (for my coffee) this week. Another fave of mine. They will be the perfect pairing!

  • Mimi

    Love these! Especially how you piped the filling before adding it to the muffins!

  • Caroline L.

    Call me cliche, but pumpkin flavored anything w/ cream cheese frosting/filling is honestly just my favorite thing!

  • kim

    YAY!! I love your original recipe and it seriously got me through hurricane Sandy/no electricity last year. Can’t wait to try this version!!

  • I have to admit I’m not quite ready for pumpkin yet, but after seeing these I kinda wish I was. In a couple weeks when the urge hits these are going to be the first thing I make. I love the look of this healthified version and I know my family will go nuts for them.

  • Warm Vanilla Sugar

    I am so happy you lightened this recipe up! I’ve made your original version several times and it is seriously the best, but you’re right, not really the best for breakfast. Great re-vamp!

  • Kaitlin

    Love the old ones and I’m sure I’ll love these! You mention freezing them… how do you reheat them? Microwave? Toaster oven?

  • stevierae5

    I just had one of these from Starbucks for the first time this past Thursday, even though it’s still too warm outside for me to go for the Pumpkin Spice Latte. I love the idea of being able to make them at home for fewer calories! 320 calories is a lot to “pay” for one delicious muffin. (Which, I agree, seem much more like cupcakes than anything approaching healthy breakfast food!)

  • I’ve been meaning to make this since…forever. But now the question is whether to make the original or the lighter version…hmmmm….

  • Michele

    This totally made my day. I make pumpkin things year round b.c I love it so much. I just discovered your original ones this summer. We LOVED them. But I also like healthier foods. I couldn’t stop being giddy this morning when I saw the updated recipe in my email. Really made my day (not sure if that makes me pathetic or not :-P )

  • Ashley Beathard Winebrenner

    To put in the freezer – do you bake them, cool them then just put in a zip lock bag? Thinking about making these for a soon to be new mom who LOVEs pumpkin

  • Nancy Long

    it’s still 90 here in St. Pete, but that won’t stop me. I still have a couple cans of pumpkin in the pantry from last winter! The neighbors are going to love me. Hubby told that the blueberry streusel muffins I sent to a neighbor got the guy in trouble. He ate them all and then kept telling his lady friend how good they were! lol

  • Nancy Long

    One question – how does ‘white whole wheat’ compare to AP/unbleached – I already have so many different flours (at least 4-5) in the house hate to buy more. Thanks

  • Jennifer

    I just made these tonight and they are delicious! I used almond meal because that’s what I had. Made the full batch of 24 just for myself – breakfast for the next few weeks just got interesting. Thank you!

  • I love this version! I could eat this for breakfast every single morning – it’s the perfect pick-me-up!

  • Jamie_MilkNCookies

    Yum! These look like quite the enjoyable breakfast treat. I love that you lightened them up, but still kept all the fantastic flavors.

  • annieseats

    To the girl who ran 18 miles this weekend, I say make the originals :)

  • annieseats

    We reheat in the microwave on a low power setting.

  • Haha point well taken. :)

  • Tiffany

    can the oil (that you replaced with applesauce) be replaced with yogurt?

  • Mandy Sosebee Mrozek

    I made these this morning for a party and they were fantastic! Thanks!

  • Regina

    I made these a few days ago and they were amazing! I even left out the eggs and substituted with ground flax seed. Never even missed it! Thanks for an amazing recipe!

  • Abbie E

    These muffins are gorgeous! I love the idea of stuffing them with cream cheese, and I love how you lightened them up. Pinning!

  • Andrea

    I can’t wait to try these. They look like a great fall treat!

  • Chrissy Lawrence

    I am enjoying one as we speak. I have made the original version many times, and I’m thrilled with this lighter version too. There is absolutely no sacrifice in taste or satisfaction. It goes so nicely with this mug of hot spiced cider I’m drinking. Thanks Annie!

  • annieseats

    Awesome! I know we thought the same, but love hearing it from someone else who knows the original well. Thanks for letting me know!

  • annieseats

    I wouldn’t recommend that. They do need a bit of oil, otherwise they are very chewy and the liners stick terribly.

  • annieseats

    It is whole grain, and therefore healthier. Definitely a pantry staple in our house, and I use it all the time in place of AP for extra fiber.

    This post I wrote has a little more info about why whole grains are good to eat: http://www.annies-eats.com/2013/07/08/baking-with-whole-grains-quick-and-easy-whole-wheat-bread/

    And here is the info from King Arthur about white whole wheat flour: http://www.kingarthurflour.com/shop/items/king-arthur-white-whole-wheat-flour-5-lb

  • annieseats

    Yes, I just freeze on a baking sheet until they are frozen, then toss into freezer bags and thaw as needed in the microwave.

  • annie, have to share these in my friday links.
    who doesn’t love a lightened up version?

  • Jennifer Kaplan

    I’m so excited to try these! I’ve made the original version at least 5 times, and everybody always raves about them. I usually make just a half batch, since I don’t need that many extras hanging around (even in the freezer), but I may have to make a full batch of this lighter version!
    Question – do you pipe the cream cheese instead of making a log because the honey makes it really runny?

  • annieseats

    No, the filling isn’t runny. This way is just much easier than the log. I no longer use that technique for the old version either because this is quicker and has less mess.

  • Sue

    I made the first version of these muffins & really enjoyed them, but I did not add them to my regular rotation of breakfast muffins to make since it was more of a dessert, This new lightened up version has changed that! My whole family agrees that it is a wonderful improvement & makes the recipe an one that I will turn to often for breakfast. Thanks Annie for the upgraded version!

  • Stephanie

    The day after I made my first batch of your pumpkin cream cheese muffins, you posted this recipe. Like you, this is one of our favorites! I’ll make several batches throughout the season. And, I’ll be honest, I only tried this lightened up version today out of a guilty conscious…. (Because I LOVE the originals) But, I will have you know, I PREFER these! :) Thanks so much Annie.

    People always are impressed with my cooking skills, but I always say, “I just do what Annie tells me to do.” You do all the hard work. :)

  • annieseats

    Wonderful, so happy to hear it!

  • Melanie

    I made these today. I didn’t have enough apple sauce, only one of the little single serving cups. I mashed a banana that was on it’s way out and put that in there. It worked great. They were super yummy!! Thanks for another great one.

  • Jess

    Love these! Might tweak them a bit next time to make the filling a little sweeter (will prob do 1 tbsp honey and 1/2 c powdered sugar). These are so amazing. Thanks for lightening up your original recipe!

  • Melinda Z.

    Oh my. I just inhaled one of these for breakfast. I’m so glad I powered through to make these after a long work day followed by an evening of studying- totally worth it! And while I’ve never tried your original, these were so delicious that I’m pretty content to stick with this version. Thanks for another foolproof recipe!

  • Tara Boffa

    How do yo ustore these if you plan to use in just a day or two ? I won’t need to freeze, but do they need to be refridgeratored due to the cream cheese?

  • annieseats

    That’s a personal judgement call. Please see the FAQ page for more info on food storage. Enjoy!

  • Haley Wheeler

    Oh man, these are so darn yummy! Another Annie recipe to add to the favorites binder. Question though – I found that after baking these that the cream cheese melted down and left a bit of an empty cavity in the middle. It doesn’t bother me, or effect the taste in anyway, I’m just curious if this has ever happened to you?

  • Stacey Johnson

    Hi Annie, I made these last weekend and they were a big hit. The only thing I had to do differently was ice them instead of putting the filling inside, because I have nowhere near the amount of freezer space it would take to freeze the filling on baking sheets. But I just saw your original muffin recipe with the rolled filling; would that work with this recipe too and be easier for me?

  • annieseats

    You can certainly do either method for the filling. I prefer this one because it is less messy and quicker, but if you don’t have the freezer space, the log works just as well. Glad you enjoyed them!

  • annieseats

    That happened in a few of mine too, but not all. I’m not exactly sure what causes it or how to avoid it. Sorry!

  • Tiffany Tott

    Just made these tonight for a friend of mine who’s due with her baby in a couple of weeks. Perfection! Thanks for the recipe!

  • Annie

    I notice that pumpkin recipes seem to call for canned pumpkin puree. I would like to know if there needs to be a difference in quantity if you are cooking and pureeing your own pumpkin. Can’t get pumpkin puree in Australia. Pumpkin cake recipes are rare here. Mostly it Pumpkin Scones (biscuits)

  • annieseats


    If you prepare it as described in this post, it is equivalent to canned pumpkin puree. Hope that helps!

  • Annie

    Thanks so much Annie I’ll give it a go :)

  • Meg

    I made these last night. I’m curious what the ‘heavy’ version tastes like, because this lightened up version does not seem to lack in flavor or moistness at all. I love that this version uses applesauce and white whole wheat flour but doesn’t have an unpleasant “healthy” taste that sometimes accompanies lightened up versions of things. And all the spices! These smell divine, and they taste like fall. The cream cheese filling in a few of my muffins oozed out the top, no doubt because I piped the filling too tall in an attempt to fit all the dollops on the lid of a tupperware container that would fit in my freezer. Awesome muffins!!

    And I have to thank you for inspiring me to try white whole wheat flour. I tried it in my all-time favorite fall dessert, zwetschgendatschi (a German plum cake), so that when I inevitably sneak a slice for breakfast, it isn’t quite as bad for me. I’m now looking forward to experimenting with white whole wheat flour in all sorts of other recipes. You rock!

  • Kat Moore

    Finally made these, Annie. I think my family is now demanding they become a tradition. Thanks for yet another great one. Even hubs, who is a notoriously non-effusive recipientof all foods (“it’s good, hon”) said they were “really good”. That means something ’round here.

  • annieseats

    Yay! So glad to hear it :)

  • Jacqueline

    Loved these! I can definitely taste the difference between these and the originals but these I can actually eat and stay on diet track for holidays! I calculated made this way with reduced fat cream cheese it’s about 215 calories and 3 grams of fiber!

  • amy

    Annie, have you ever tried to make these with any other kind of flour, coconut, almond, etc.? Or even for 1/2 the amount? Just curious if you’ve tried it and how it changes the texture.

  • Annie

    No, I haven’t experimented with other types of flour. Let me know how it goes if you do!