Chocolate Chocolate Chip Muffins Recipe (With Optional Peanut Butter Center)

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This Chocolate Chocolate Chip Muffins recipe has an optional peanut butter center you will love!

Clean eating is great. I love my chicken and veggies. But as you may or may not know, I am also sometimes a die-hard dessert fanatic. There are moments where I just can’t help myself.

One of these Chocolate Chocolate Chip Muffins sits broken open, showing melty chocolate chips inside, warm out of the oven.

Dessert is like a cool waterfall on a hot summer day. Like a warm pile of laundry out of the dryer when you’ve just come in from shoveling piles of snow. Like a hot pot of coffee on a morning when you have to roll out of bed onto the floor with a thud just to wake yourself up enough to crawl into the kitchen and grab your mug.

Yep, dessert is necessary for any person hoping to maintain some semblance of sanity. After weeks of sticking to an eating plan like it’s going out of style, I need a treat that feels completely indulgent without actually damaging all my hard work.

A chocolate chocolate chip muffin, broken open and showing a peanut butter center.

A few extra calories? Perhaps. But eat these in moderation and you won’t be gaining any weight from them either. They are decadent, but they’re clean!!


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A chocolate chocolate chip muffin, broken open and showing a peanut butter center.

Chocolate Chocolate Chip Muffins Recipe

Delicious chocolate muffins that give you the options of all chocolate, or chocolate with a peanut butter center! Yum!
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Course: Dessert
Cuisine: American
Prep Time: 15 minutes
Cook Time: 30 minutes
Total Time: 45 minutes
Servings: 18 muffins
Calories: 153kcal
Author: The Gracious Pantry


  • Standard muffin pan


  • 1 1/2 cups whole wheat pastry flour
  • 2 tsp. baking soda
  • 1/2 tsp. ground cinnamon
  • 1/4 tsp. ground black pepper
  • 1/4 tsp. sea salt
  • 1/2 cup unsweetened cocoa powder
  • 1 cup dark chocolate chips (I use the Lily's brand)
  • 2 large egg whites
  • 1/2 cup honey
  • 1/4 cup oil (light flavored)
  • 1/2 cup unsweetened almond milk (any milk will work here)
  • 12 tbsp. peanut butter (optional - if using - 2 tsp. per muffin - no sugar added)


  • Preheat oven to 350 degrees F.
  • Line your muffin tin with muffin/cupcake papersIn a medium mixing bowl, whisk together the flour, baking soda, cinnamon, pepper, salt, cocoa powder and chocolate chips (Coating the chocolate chips in flour helps keep them from sinking to the bottom of your muffins during baking).
  • In a large mixing bowl, whisk together the egg whites, honey, oil and almond milk.
  • Pour the flour mixture into the liquids and blend well with a wooden spoon.
  • Fill your muffin papers half way with batter and place in the oven. If you want the peanut butter centers, fill the papers a 1/4 of the way (being sure to evenly distribute the batter over the bottom of the muffin paper), drop the peanut butter in the center, then cover the peanut butter entirely with the rest of the batter. If you use the peanut butter, your muffin papers will be closer to 3/4 full.
  • Bake for 20-30 minutes. Test with a knife or cake tester. Be aware that you may pull out some melted chocolate from the chocolate chips. So examine it carefully to see if it's melted chocolate or raw batter if the stick or knife does not pull out clean.
  • Cool on a wire rack and serve.


Please note that the nutrition data given here is a ballpark figure. Exact data is not possible. Data does not include optional peanut butter.


Serving: 1muffin | Calories: 153kcal | Carbohydrates: 22g | Protein: 3g | Fat: 7g | Saturated Fat: 3g | Cholesterol: 1mg | Sodium: 209mg | Potassium: 147mg | Fiber: 2g | Sugar: 11g | Vitamin C: 1mg | Calcium: 47mg | Iron: 1mg

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  1. OMG Tiffany, these look awesome! I definitely will be trying these tomorrow after shopping 🙂

    1. The Gracious Pantry says:

      Kim – Fabulous!! Hope you enjoy them!

  2. Sounds delicious! Much as I love to eat healthy and relish veggies and healthy grains, I can’t resist dessert! This sounds like a great way to sneak in some dessert without going overboard or reversing all those well-intentioned meals! Thanks for sharing!

    1. The Gracious Pantry says:

      Laura – You’re a woman after my own heart! I love dessert too!

  3. OMGosh, Can’t wait to make these. You spoil us and our families think we are spoiling them, little do they know these are really not bad for you.!!!!! Every one of your recipes that I have made for my family has been raved over. I feel like I should be paying you for these great recipes.

  4. OMG sounds fabulous, can’t wait to try!!! Can whole wheat flour be sub’ed? how about the oil.. can olive oil or applesauce work instead? thanks…. OOOO they look good 🙂

    1. The Gracious Pantry says:

      Mere – Yes, you can use regular whole wheat flour, but the muffins will end up being a little more dense. You can also substitute with olive oil if you wish. I don’t recommend using apple sauce in this one only because they may come out to “rubbery”. Hope that helps. Enjoy!

  5. This looks amazing! Have you tried making cake lollipops? I was thinking it would be an amazing clean treat in a small portion.. the new ones at Starbucks peaked my interest..

    1. The Gracious Pantry says:

      Holly – I haven’t seen those yet. But that sounds interesting!

  6. Just made this with my 10 year old daughter…these are AMAZING! Love them! Cheers!

    1. The Gracious Pantry says:

      Sheridan – Fantastic! Thanks for trying my recipe. Enjoy them!

  7. Christina says:

    I made these with my 11-year old stepson on Sunday evening and they turned out fabulous!! Thank you for the new “clean” dessert recipe. They’ve been a huge hit.

    1. The Gracious Pantry says:

      Christina – Yay!!! I’m so happy you enjoyed them!

  8. I tried these yesterday and although they tasted great they were very dense and a little dry. Mine were not fluffy & cake like, the way your picture looks. I used WW pastry flour, so not sure where I went wrong.

    1. The Gracious Pantry says:

      Reneau – Hmmm…
      Did you maybe mis-measure the milk or oil? If you try the recipe again, maybe add a 1/4 -1/2 cup of unsweetened apple sauce. That will always add moisture.

  9. thezestyonion says:

    DELISH!!! My girlies are on Spring Break this week, so we tried this recipe ~~ they loved, loved these ~ they also said that one cupcake was filling (so they weren’t coming to me 5 minutes later asking me for more food while on a sugar high like with most “normal” cupcakes). Two Yums Up!!

    1. The Gracious Pantry says:

      TZO – That’s great! It’s amazing how much more satisfying healthy treats are, isn’t it? I’m so happy everyone enjoyed them!

  10. Where can I find grain swetened chocolate chips? thanks 🙂

    1. The Gracious Pantry says:

      Tara – I get mine at the health food store. But there is a brand called SunSpire that makes them. I believe they sell at whole foods if you have one near you. If not, you can maybe find another location on their web site.

  11. We loved these! My daughter said they are the best muffins she’s ever had and that I should go on cupcake wars. 🙂

    1. The Gracious Pantry says:

      Lisa – LOL!!! That’s wonderful!! It’s always nice to hear when kids enjoy my recipes. Lets me know I’m doing something right! 😉

  12. THESE WERE AHHH-MAAAAAZING!!! My hubby makes me a cake each year for my birthday, but since I’ve gone ‘Clean’ (the only way to live) and gluten-free (not by choice) I wanted something else this year that was both delectable and healthy. These hit the spot! We substituted the flour with Pamela’s gluten-free pancake mix and made two versions: your chocolate/peanut-butter one listed above and a plain version with an almond butter center. BEST.BIRTHDAY.EVER!!! Thank you for this wonderful site; I’m completely hooked!

    1. The Gracious Pantry says:

      Cyana – Fantastic! I’m so happy you enjoyed them! And HAPPY BIRTHDAY!!!!! 🙂

  13. Do you have a recipe for a clean version of peanut butter frosting? That would be amazing on these.

    1. The Gracious Pantry says:

      Lauren – Not yet, but I have a recipe in mind. It will be in a future post.

  14. DanaYourHugeFan says:

    If I have failed to yet ask for your hand in marriage, let it be known that I am now officially asking you to marry me, and that I love you. I’m not gay and I’m already married, but I will make the exception for you.

    1. Anonymous says:

      Dana – ROFLMBO!!!!!!!!!! LOL!!!!!! I’m guessing you liked the muffins? HAHAHAHAHA!!!

  15. Anonymous says:

    Miranda – Glad you like them!
    It’s possible. Everyone’s oven bakes a little different.

  16. OMG!! AMAZING!!! I can’t wait for my kids to try these out tomorrow.

    1. graciouspantry says:

      Missie – I hope everyone enjoys them!

  17. graciouspantry says:

    Evelyn – Depends. If you are only on week 2 of clean eating, then it’s possible that these would still seem very dense to you. The longer you eat clean, the more this density becomes the norm, and you will end up enjoying it. However, if there was really an issue here, you might try using WHITE whole wheat flour next time. The pastry flour usually provides the least dense texture while the white whole wheat flour provides a more “bready” texture. But it’s worth experimenting to see what you like best. There could be a variety of things that “went wrong”, but I have a feeling that it may just be that your taste buds haven’t changed yet since you are only 2 weeks into it. Just a hunch.

  18. Can I use coconut milk? I’m allergic to the almond & soy milks.

    1. graciouspantry says:

      Sure! But I would use the light version.

  19. Hmmm, I wonder if I can make these as mini muffins?

    1. graciouspantry says:

      You may have to reduce the baking time a bit, but it should work fine.

  20. Made these and I have to be honest.. Very bland. I would try adding some sweetener and definitely include the peanut butter centers (a good amount). Not bad for breakfast but in was expecting something sweeter.

    1. graciouspantry says:

      If you are used to eating very sweet and sugary things, these will not be sweet to you. But once you cut back on sugar intake, these are VERY sweet. I promise. 🙂

  21. These look A-mazing!! I was wondering if I can substitute the oil with a different kind of oil I might have on hand? Thanks!

    1. The Gracious Pantry says:

      Sure. Any light flavored oil will work. Enjoy!

  22. These look so yummy, but i tried them and the cocoa powder just seems to outweight the rest, i cant get rid of that ‘bitter’ taste! any suggestions?

    1. The Gracious Pantry says:

      What kind of cocoa powder did you use? Cheaper brands tend to have that bitter after taste. It’s always good to invest in good quality cocoa powder.

  23. where do you find grain sweetened chocolate? i cant find them anywhere!

    1. The Gracious Pantry says:

      I get these. You could contact the company to find where they sell in your area, or try amazon. They seem to have everything.

  24. Could I use PB2 in the center of these muffins? Reconstituted of course.

    1. The Gracious Pantry says:

      You need the oil to keep things moist. I’ve never used PB2, but I’m guessing, no.

  25. Hi– I am relatively new to your blog, I have been clean eating for about 3 years now and was looking for some inspiration with desserts… I was wondering what the black pepper does to this recipe?

    1. The Gracious Pantry says:

      Danielle – For me, it brings out the kick in the chocolate a bit more. But you don’t have to use it if you don’t want to.

  26. Thankyou! I ended up using the black pepper, I was just curious bc I’ve never used it BAKING before. I like to stay true to a recipe the first time to see if I want to substitute anything else later! But everything was delicious and I will definitely be making these again, my 3 year old devoured them 🙂

    1. The Gracious Pantry says:

      Danielle – My pleasure! 🙂

  27. Ashley Baker says:

    I made these last night and they were so good! My kids loved them! I did put about a tsp of homemade peanut butter in the center and my recipe only made 12. I know by making bigger muffins, the calorie count was much higher- like 215 a muffin! Do you have any recommendations on how to make them a little healthier? How much could I cut down on the honey and oil without affecting the taste and texture too much? Thanks!

    1. The Gracious Pantry says:

      Ashley – I’m not sure what your definition of healthier is. Are you sure you measured everything correctly? That just seems like a big drop from the 18 I got.

  28. I think I did, but who knows? I have made some mistakes in the kitchen before 😉 By healthier, I mean lower fat and sugar. How much could I reduce the oil and honey without affecting the taste? Or, could I use a substitution?

    1. The Gracious Pantry says:

      Ashley – You could probably reduce the honey by half, but I wouldn’t go too much lower on the oil. It gives the muffins some moisture. It’s 4 tablespoons, so maybe try 3 tablespoons?

  29. I need to make breakfast in bulk to last my husband and I all week! I want something on obviously healthy but something that will keep us full and give good nutritional values because I’m breastfeeding! So is this a good idea or is there a recipe you can think of off the top of your head that would be good to try for us?

  30. Sandy Wessel says:


    I love your website and your recipes, but I did see you included soy milk as an option in the ingredients… why went soy milk is not clean?

    1. The Gracious Pantry says:

      Sandy – You will find it in my older recipes from when I first started eating clean and thought that soy was a good option. You won’t find it in my recipes now.

  31. Hi! I know you’re ALWAYS answering questions about pastry flour, and here’s one more! I have tried and tried to find whole wheat pastry flour near me, but haven’t had any luck. However, I did find whole grain pastry flour. Do you think there will be a noticeable difference if I use the whole grain pastry flour?

    1. The Gracious Pantry says:

      Jennifer – What grains is it made with?

  32. The ingredients list is: Organic whole grain soft wheat flour. I’m not sure how much help that is!

    1. The Gracious Pantry says:

      Jennifer – That’s it? I’ll have to check, but it seems clean to me.

  33. What qualifies this as clean eating. Starting on this path and I’m a little confused?

    1. The Gracious Pantry says:

      Alesha – Here is a description of clean eating: With this recipe, it’s all whole food ingredients. The only thing that is not 100% clean is the chocolate chips. You will find that with things like this, mild exceptions are not the end of the world. You can also make your own and I hope to do a post on that soon. But until then, I chose the “cleanest” chips I could find.

  34. JenniferSheppard says:

    We made these for breakfast this morning. They were a tad dry but I also baked them on the long end of the suggested time. Next time I make these I will try agave(just to taste the difference) and bake them for about 16-18 min. My oven bakes hotter than normal. My husband had a MAJOR sweet tooth and these seemed a little “bland” to him. I might try a little more honey/agave next time. It’s a hard task but I’m trying to weine him off of so much salt and sugar. Also, is Hershey’s cocoa powder consider a “cheaper” cocoa and if so, what brand do you recommend? Thanks again for all you do, you really do make this transition easier.

    1. The Gracious Pantry says:

      JenniferSheppard – I have used Hershey’s. I try to buy organic stuff though. Seems like it’s always better quality.

  35. Can I use olive oil or something else in place of the safflower oil? I don’t have any safflower oil in my pantry right now.
    Thanks for your help! Can’t wait to try this recipe!

    1. The Gracious Pantry says:

      Jen – Sure! I just chose that one because of the light flavor.

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