Chocolate Chip Pumpkin Cheesecake Muffins

Welcome to my favorite muffin recipe of all time! I’ve made Double Chocolate Greek Yogurt MuffinsGreek Yogurt Collagen Chocolate Chip MuffinsSuper Easy Chocolate Chip Banana Walnut Muffins, and Pumpkin Chocolate Chip Muffins, and all 4 of those recipes were some of my favorite muffin recipes. But they have to step aside now because THIS RECIPE reigns supreme. It’s fantastic. The muffins are moist (stop being grossed out, it’s the best word for the job), fluffy, and they are amazing for leftovers. Sometimes paleo baked goods can get a little weird after a few days, but not these. When I first made these, I loved them so much that I packed the leftovers with me on one of my recent trips. And they still held up even when they weren’t in the fridge. Sketchy? Maybe. But no food poisoning for me!

PaleOMG Chocolate Chip Pumpkin Cheesecake Muffins

I know it’s annoying to be that pumpkin spice basic b*tch, but I really do adore pumpkin everything. I think it’s the cinnamon in the spice mix. I just simply adore cinnamon. It makes any comforting dish even more comforting. I just recently started adding cinnamon to my coffee and it’s life changing. And yes, I know I’m behind the times, but I’m glad I finally figured life out. Because now I add cinnamon to my coffee every morning and I wake up excited for the day. I’ve always been an annoyingly happy person in the mornings, but now it’s even worse.

PaleOMG Chocolate Chip Pumpkin Cheesecake Muffins

Speaking of loving pumpkin, I’m loving a lot of things right now. Here are some of the things I’m loving the most –

  1. My Nespresso Vertuo. Every morning I wake up excited to be alive because I know I’ll have the best cup of coffee in about 3 minutes. I make mine with heavy cream, collagen, cinnamon and stevia and it’s truly the best thing ever.
  2. A restaurant near me called Olive & Finch. Because I recently started eating their salmon plate that comes with a red curry sauce and I get sautéed kale instead of farro. It’s my new favorite thing that is giving me life around lunch time.
  3. My instant pot. Because now that it’s dropped down below 50 degrees, I’m constantly cold and in need of soup. And my instant pot makes soup dreams come true. Like with my Instant Pot Creamy Gnocchi Soup and my Instant Pot Creamy Tomato Pesto Soup.
  4. My groceries being delivered. It’s the new highlight of my week at the moment as I mentioned on Tuesday. I started using Amazon Prime Now just this week and it’s life changing. I say life changing a lot, don’t I? Either way, it is. I have so much extra time in my week now that I’m not hitting up the grocery store almost every day. I love it so much!
  5. The fact that I leave for New Zealand is THREE FREAKING WEEKS!!! AHHHHHHH!

PaleOMG Chocolate Chip Pumpkin Cheesecake Muffins

Ok wait, with the good comes the bad. And I’m really good at disliking things. Here are the things I’m not digging lately –

  1. My rental car that smells like smoke. Who smokes cigarettes these days? Who smokes in rental cars? Who thinks smoking is cool? Have they never seen the TRUTH commercials?! COME ON!
  2. The current bloat I have from drinking over the weekend. Drinking is so damn bad for you. And sure, it’s fun and I enjoy a few spicy cocktails, but getting back to normal is a pain. I hate looking puffy and feeling like I look tired. And I honestly didn’t drink crazy amounts over the weekend, just a handful. And I still look fluffy AF. I’ve decided to not drink again until I’m in New Zealand on vacation. Every time I drink, it’s always so eye opening how bad alcohol really is for you. Isn’t it crazy it’s legal?!
  3. My anxiety level about leaving in 3 weeks. I’m trying to get all my work done ahead of time so I don’t have to work much while I’m in NZ, but getting that much work done is tough. There are not enough hours in the day!

PaleOMG Chocolate Chip Pumpkin Cheesecake Muffins

Luckily my likes outweigh my dislikes. But anywho, if you want to see a quick video on how to whip these up, I’m going to make them on my IG stories today. But act quick because IG stories die after 24 hours. Along with my soul. I’m kind of hating instagram at the moment. It’s giving me absolutely no joy when I open up the app. So I’m spending less and less time on there. Which totally blows because I use to love instagram. Oh how social media dies so quickly. But I am trying to share as many cooking videos as possible to make sure you guys have as much food content as possible. People asked for more recipes on my IG stories so I’m trying to give as much of that as possible. Which hating every moment on there. It’s a tough balance. I guess instagram should go on my not digging list, after all. Ok I have a dog to walk! Byeeeeeeee!

PaleOMG Chocolate Chip Pumpkin Cheesecake Muffins


Chocolate Chip Pumpkin Cheesecake Muffins

  • Author: juli
  • Prep Time: 15 minutes
  • Cook Time: 30 minutes
  • Total Time: 45 minutes



For the pumpkin:

  • 1/4 cup coconut flour
  • 1/2 cup tapioca flour
  • 1/2 cup maple or coconut sugar
  • 1 tablespoon pumpkin pie spice
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon baking powder
  • pinch of salt
  • 2 large eggs
  • 1/3 cup pumpkin puree
  • 2 tablespoons almond milk
  • 1 teaspoon vanilla extract
  • 1/4 cup mini chocolate chips

For the cheesecake:


    1. Preheat oven to 350 degrees F. Line a muffin time with parchment paper liners and spray with coconut oil spray.
    2. In a large bowl, whisk together coconut flour, tapioca flour, maple sugar, pumpkin pie spice, baking soda and powder, and salt.
    3. Then add eggs, pumpkin puree, almond milk, and vanilla extract and use a spatula to mix until everything is completely combined and smooth. Fold in chocolate chips.
    4. In another bowl, add all ingredients for the cheesecake (except for the chocolate chips) and  beat together for 1-2 minutes until combine. Fold in chocolate chips.
    5. Use a cookie scoop to scoop the pumpkin batter into 12 muffin cups. This should fill each cup up about 1/3-1/2 full.
    6. Then use the cookie scoop to scoop the cheesecake layer on top of the pumpkin layer in each muffin cup.
    7. Using a knife, toothpick or anything else, swirl the two batters together to combined. 
    8. Place in the oven to bake for 30 minutes.
    9. Remove from muffin tin and place on a wire rack to cool.
    10. Store in closed container in fridge. 


    *I used Kite Hill brand

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    PaleOMG Chocolate Chip Pumpkin Cheesecake Muffins

    PaleOMG Chocolate Chip Pumpkin Cheesecake Muffins


    More Pumpkin Love!

    Pumpkin Pie Smoothie Bowl

    Pumpkin Crumb Pancakes


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    Oh, Hi! I’m Juli.

    I’m a food hoarder. And a really bad dancer. If you don’t know me well, you will probably not understand my humor. Therefore, I apologize ahead of time. Thanks for listening to my ramblings of my ever-changing life and trusting my kitchen mishaps. Your trust in me is appreciated.


    58 thoughts on “Chocolate Chip Pumpkin Cheesecake Muffins”

    1. I’ve been waiting for you to put out this recipe ever since you put out the teaser photo! Can’t wait!! I made your cheesecake brownies and they were the best. Cheesecake anything! And now with pumpkin! Yummm!! Thanks Juli!!!

    2. I’d like to add that I agree with Instagram – I’m finding myself on it less and less lately. Now it all shows me are pictures of people’s kids, like Facebook, since they prioritize my FB friends first on my feed. I miss the days where it just showed you everything in the order it was posted. Why can’t it just be like that anymore???

      I check out your blog every week to read your posts, mostly through your emails, which makes me sound old fashioned lol. But seriously, the older I get (I’m 32) the less I am caring about posting or going on social media. I know you pretty much have to for your business. Do you ever wish you didn’t have to be on social media for your job?

      Also, you have super long names for muffins lol – but these look fantastic!

      1. good to hear that’s how you get my content because i work hard on that newsletter every week! and YES. every day i wish social media wasn’t my job. i would be off it all together if it wasn’t part of my business.

        1. Maybe you’ll get to a point when you can hire someone to be in charge of your social media? I’d be happy to volunteer for the job! 😉

    3. Already made these bad boys!!! They are a winner….along with your others!!! Definite repeat!! Thanks for the awesome recipe!!

    4. These look so good! I can totally relate to you about the looking puffy and old after drinking alcohol situation. I enjoy wine, and I save those calories for Friday and Saturday, because I like to feel my best during my workouts, but I usually have 2-3 glasses maybe and the next day I look like the Stay Puft marshmallow man…and my face is a whole other story!

    5. So far, my fav muffins of yours are the collagen chocolate chip ones. YUM! Can’t wait to make these!!!
      You showed a recipe book with instant pot and air fryer recipes, I think on your insta stories. Would you please tell me what book it was again? I can’t find where you posted it. Thank you!!

    6. I can’t have almonds right now. I am not sure I am ready to go full on real cream cheese. Do you think a thick, greek yogurt would work??

    7. Juli- These look amazing… ! Can I sub flour of any kind and can I use same measurement of regular cream cheese?
      PS- your blog keeps getting better and better! Love following your stuff.

        1. These came out PERFECTLY and I am not a baker!! FYI- I subbed all flour for Bob’s Red Mill Paleo flour, regular organic sugar, regular Philadelphia cream cheese (because- boyfriend). Sooo yum and satisfied the “basic” pumpkin everything addiction. Will make again. Thanks!

    8. Hey there! I can’t wait to try these cupcakes! I might take them to my work party next week. I saw in your post that you are going to New Zealand soon. If you are going to be near Auckland, you should go to this amazing bakery, Magnolia Bakery. I follow her on insta and she makes the most amazing looking GF baked goods! Have a blast!

    9. Yum! Need to make these over the weekend after I get a facial and can’t leave my apartment or I might scare people….you get what I mean Juli;)
      Also, all these pumpkin recipes make me wonder what you’re doing for the holidays? Will you be in Omaha at your in-laws by chance? Have you ever thought of doing a meet-up there? I’d love to come since I’m in the area!

      1. no more omaha for us. my MIL comes out to Denver nowadays since most of us are out here along with my own family. so no omaha meet-ups planned for me.

    10. Juli, you’re a freaking genius. These muffins are EVERYTHING. I’ve made probably hundreds of muffin recipes at this point but this morning my husband text me and said that these are the best muffins I’ve ever made — we both LOVE them! They’re the BEST! 🙂

    11. Kimberly Bortnick

      Hi Juli!
      My name is Kimberly, and I live in Nelson, on the South Island, NZ. I’ve been Paleo for nearly 4 years and have your 3rd cookbook and sooo many of your recipes saved. Love the newsletter as well. I am an expat from San Diego’, and you are going to fall in love with our country !! I did my first visit, and moved here 12 years ago. Never looked back. I’m a retired nurse, teach yoga, and love to cook, especially Paleo. I feel better than I ever have , and am more fit each day. If you happen to pass thru Nelson, and I highly recommend it, we have the best weather, beaches, great restaurants and wine. We are about an hour fromAbel Tasman Park, the smallest, but one of the most beautiful national parks here. Stunning coastal hikes! You will love the Kiwi people and the culture. The beauty is u surpassed. And if you pass thru Nelson, drop me text. I’ll show you around and give ya a few tips for your holiday if you want.
      Cheers, and thank you for all your hard and inspiring work ,

    12. Made this in a loaf because I’m special and didn’t realize I did not have cupcake pans.
      Subbed almond flour for the tapioca flour and doubled the baking time since I did it in a loaf pan.
      Next time, I’ll layer the cream cheese filling in the middle.
      So fuckin tasty! Thanks J!

    13. My local stores were all out of Kite Hill cream cheese (said it was a supplier issue) so I made this with a different brand of dairy free cream cheese that was made with coconut. They did NOT turn out. I wish i could show a picture here but the top part was oily gooey weirdness 🙁

    14. Good but a lot of work and we only yielded 10 muffins! We even nutri bulleted the cream cheese mixture. Woulda liked more pumpkin so will adjust and at least double for the effort put in-
      Ps made along with the sausage soup posted which turned out amazing although I also tweaked that recipe too! Small kitchen crazy results! Thanks-

    15. These are HANDS down the best pumpkin muffins EVERRR. And my second fav are your OG pumpkin chocolate chip muffins. I was a little nervous that the pumpkin batter was too dry compared to a lot of my paleo batters but they turned out PERFECT! Super easy, the best texture and MOIST (gross but accurate). Now I must try to not make these bi-weekly. Thanks Juli! 🙂

    16. Just made these and they were AMAZING!!!!! I made them for work friends but may have to “forget” them at home! So dang good!

    17. These were amazing – everyone in my house loved them! I want to make them for Thanksgiving but we are serving someone with a nut allergy. I saw above that someone didn’t have luck with coconut milk cream cheese, but was wondering if any other non-dairy cream cheese(s) are good options to try. Thanks! Love all your recipes (made the fried rice last night, which is also a winner.) Thanks!

    18. I’ve been salivating over the pictures of these forever and I’m SO excited to try making them. My only [stupid] concern is that my boyfriend doesn’t like pumpkin-y things. I know, it’s almost a deal-breaker. 😉 But do you have any suggestions of what I could use in place of the pumpkin puree and spice? Like some kind of apple butter maybe? I know it completely changes the whole recipe. He’s the worst. Unfortunately I love him too much.

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