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

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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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    1. Kristin says:

      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! 🙂

      1. juli says:

        woooooot wooooot! glad you loved them!!

    2. Cindy says:

      Hello! I was wondering if you have ever made these with cashew cheese? Love the Blog and the recipees. Keep’m coming.

      1. juli says:

        not sure, i haven’t tried it that way!

    3. Lindsey Harris says:

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

      1. juli says:

        awesome!! so glad to hear you liked them!

    4. Lucy says:

      Would you happen to have the nutrition information for these?

      1. juli says:

        nope, but you can easily find that information out by plugging it into a nutritional calculator yourself!

    5. Ali says:

      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!

      1. juli says:

        i’ve only ever tried them with almond milk cream cheese so i can’t say for sure

    6. Liliana Aranda says:

      I can’t find maple sugar, what is a good alternative?

      1. juli says:

        coconut sugar, it will just change the color to the cheesecake layer a bit

    7. Mareen says:

      The biggest complaint I have about this recipe is that I cannot eat just one. It is sooo good.

      1. juli says:

        hahahaha i feel the exact same way Mareen

    8. Vanessa says:

      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.

      1. juli says:

        you could use pureed butternut squash or sweet potato puree instead!