Healthy Chocolate Chunk Molasses Gingerbread Cookies

These healthier chocolate chunk molasses gingerbread cookies are chewy, soft and filled with the flavors of the holidays.

Healthier chocolate chunk molasses gingerbread cookies are soft, chewy and filled with all the flavors of the holiday.

*Post updated 12/6/2017 to include a video on how to make these healthy chocolate chunk molasses gingerbread cookies. Photographs and content below are original to when this was published in December 2012. This cookie recipe is a personal favorite. As someone who isn’t super keen on gingerbread, the addition of chocolate chunks to this cookie completely transforms the classic combination of gingerbread and molasses into a cookie worth eating: soft, chewy and with just enough holiday spice. Hope you enjoy some this holiday season! SCROLL DOWN TO WATCH THE VIDEO!

Up until last Friday I was positive that I would never like the whole molasses gingerbread cookie thing. I can get behind many a cookie but that combo just wasn’t doing anything for me.

Then I saw a chocolate molasses gingerbread cookie recipe similar to these just a bit more indulgent and being the good wife that I am, knew Ulysses would love them (his love for gingerbread baked goods is enough for the two of us) so I decided to bake them up for his return home on Friday night.

And now, November 30 will forever be the day my molasses gingerbread hatred turned to love. No awkward in between friendship stage, straight to love. That’s how I roll. Or maybe it’s just lust? Jury’s still out on that.

Either way, we’re a thing now with the creation of these soft and chewy chocolate chunk molasses gingerbread cookies.

Make these easy chocolate chunk gingerbread molasses cookies for a slightly healthier way to indulge this holiday season.

Thanks to a little help from a good friend called dark chocolate.

That was the missing link.

I took the weekend off from working out, happily ate 4 or 5 (which took massive amounts of self control) of the cookies and when Ulysses left again on Sunday night, I froze the remaining 18 or so.

Somehow frozen = off limits to my brain. But then Monday night rolled around and my nightly tea was incredibly pathetic without an accompanying cookie.

So I made the batter for this healthier version of those molasses gingerbread cookies.

Looking for more holiday cookies? Try out these almond chocolate thumbprint cookies, dark chocolate amaretto fudge cookies or, one of my favorites, these chocolate dipped cashew almond butter cookies with candied sage (<– they’re so festive!)

Soft, chewy and bursting with chunks of chocolate, these molasses gingerbread cookies are a must make this holiday season.

Honestly, they were a total experiment.

Could molasses gingerbread cookies actually be health-ified to a state where I can eat the whole batch and not think twice?

Because as awesome as the other ones were, a stick of butter and a cup and a half of sugar is not something I need or want to be eating regularly.

These molasses gingerbread cookies with chocolate chunks will become a holiday favorite. Soft, chewy and a bit healthier than the classic!

Some experiments work, some don’t.

These kicked ass.

Without trying to sound a bit cocky, I’m totally floored that they came out as well as they did. They’re soft and chewy with the perfect balance of spicy molasses flavor to chocolate and yet there’s a mere 1 tablespoon of coconut oil and 1/4 cup honey in them as far as the fat and sugar go.

I don’t get it, but I’m not complaining.

Molasses gingerbread cookies

I know I’m going to get comments on whether you can sub the spelt flour to all almond flour to make these completely paleo (assuming you don’t roll them in sugar before baking) and while I haven’t tried it, I’m going to say yes, I think you could.

No promises, but I think it would work. And if you don’t care about the paleo thing, all purpose or whole wheat pastry would probably work in place of the spelt too.

Now that that’s out of the way…


Yield: about 1 dozen

Healthy Chocolate Chunk Molasses Gingerbread Cookies

Healthy Chocolate Chunk Molasses Gingerbread Cookies

These healthier chocolate chunk molasses gingerbread cookies are chewy, soft and filled with the flavors of the holidays.

Prep Time 2 hours 10 minutes
Cook Time 8 minutes
Total Time 2 hours 18 minutes


  • ¾ cup almond flour
  • ½ cup spelt flour
  • ½ teaspoon baking soda
  • 1 teaspoon cinnamon
  • ½ teaspoon ginger
  • 1/8 teaspoon salt
  • 2 tablespoons molasses
  • ¼ cup honey
  • ½ teaspoon vanilla extract
  • 1 egg
  • 1 tablespoon melted coconut oil
  • 1/3 cup dark chocolate (72% or higher), chopped
  • 2 tablespoons sugar
  • ½ teaspoon cinnamon


  1. In a large bowl, combine all dry ingredients (almond flour, spelt flour, baking soda and spices).
  2. In a small bowl whisk together remaining wet ingredients until completely smooth.
  3. Add wet to dry ingredients and mix together until fully incorporated.
  4. Add chocolate chunks and fold into batter.
  5. Cover and refrigerate for at least 2 hours or overnight.
  6. Once chilled, roll about 1 tablespoon of batter into a ball.
  7. If coating with sugar mixture, combine sugar and cinnamon in a small bowl and roll ball until covered.
  8. Place on a baking sheet lined with parchment paper or silpat.
  9. Bake at 350 degrees for 8 minutes.
  10. Remove cookies from oven and press down on the top of them with a spoon for that signature molasses cookie wrinkle effect.
  11. Let cool on baking sheet for 5 minutes before transferring to a cooling rack.
  12. Store in an airtight container.

Nutrition Information:



Serving Size:


Amount Per Serving: Calories: 153Total Fat: 7gSaturated Fat: 3gTrans Fat: 0gUnsaturated Fat: 4gCholesterol: 16mgSodium: 83mgCarbohydrates: 21gFiber: 2gSugar: 14gProtein: 3g

This website provides approximate nutrition information for convenience and as a courtesy only. Nutrition information can vary for a variety of reasons. For the most precise nutritional data use your preferred nutrition calculator based on the actual ingredients you used in the recipe.


  1. Jennifer @ Peanut Butter and Peppers

    I saw those cookies to on Averie’s site and I bookmarked them! She made them look amazing that I wanted to reach through my screen and grab one! I absolutely love your version! I like that it’s a healthier version and that it only makes a dozen! I have no control I’d eat a dozen in a day!!!

  2. Aparna B. @ Not A Leaf

    I’m with you. I love gingerbread flavorings and the smell (especially in candles), but I’m not a big gingerbread, molasses person. There are a lot of cookies out there that taste better to me. However, you have me intrigued. If you made these and liked them, then perhaps I too can cookie convert.

  3. Shannon

    These look delicious and scream holiday to me. I was looking for some sort of new, different cookie to try this weekend. I’m very excited to have found this recipe!

  4. Channing

    So excited about this recipe! I’ve been craving gingerbread men but I know what an insanely huge amount of butter goes into them. Can’t wait to try these, thank you for posting!! :D

  5. Amanda

    YUM. The texture of these sounds incredible. I’m thinking I need to attempt a vegan version the next time I have a cookie craving (which will probably be later today, if I’m being honest). I should probably take a little break between sweets though, considering I’ve been living off of brownies for the last two days.

  6. Michele

    Hi Gina, I’m new to your website. I’ve got a question about the “coconut oil” in your last few recipies. Why chose that oil? Can I substitute?

    1. Running to the Kitchen Post author

      Coconut oil is pretty common in paleo cooking/baking. It’s got a list of benefits including being a very stable oil at high temps and it’s high lauric acid content (which is known to help fight disease). That being said, you can definitely substitute. If it’s in a cooking recipe, I would normally use extra virgin olive oil. In baking, probably canola.

  7. Kelly @ No Sugar Sweet Life

    I suck at making cookies, as mentioned in today’s blogpost… the only ones I’ve made recently turned into the most hellishly expensive “dog treats” ever…haha. SOOOOO, I’m excited to try your recipe knowing that it WILL turn out great, even with low sugar, low butter :) Thanks!!!

  8. Catherine

    Was just thinking tonight: could I adapt ginger cookies to use spelt, coconut oil and agave? And here you are already figuring it out for me!
    Making tonight- baking tomorrow. Will report back if they work with agave. No honey in the house.

  9. Alex

    These look delish. Would it be possible to substitute honey or brown sugar for the molasses? And if I use Trader Joe’s almond flour, would they come out ok? Thank you!

    1. Running to the Kitchen Post author

      TJ’s almond flour will work fine. Not sure on the honey or brown sugar substitution, I haven’t tried it that way. Molasses gives cookies a good “chew” that I don’t think you’ll get from either of those.

  10. Kylee

    Just made these! Haven’t taste tested yet, but I subbed all-purpose flour for the spelt and I’m not sure if that is the cause but my cookies were very hard to roll into a ball even after being chilled for ~20 hours (super sticky!) and then they spread out a lot more than yours looked in the pictures! I also made a double batch, so that could be it too. Anyways that’s my experience but they look and smell delicious! It’s also possible that I doubled something incorrectly at some point and that’s the problem. Anyways they’re great! AND the batter is really good ;)

    1. Jo

      Same thing happened to me when I made them with all-purpose flour and I followed the recipe exactly. I assumed “serves 12” meant 12 cookies but they were bigger than 1 tablespoon. Could she have meant 2 cookies as one serving? Anyway they were still way undercooked after 8 minutes so I baked longer and they were as flat as crepes. The taste was great though so I’m going to try the unhealthy cookies these were based on.

      1. Running to the Kitchen Post author

        By using all-purpose instead of spelt and almond flours, you’re changing the largest component of the recipe, of course the outcome will likely change.

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  12. Melissa @ Fit 'N' Well Mommy

    Wow, these look heavenly! I love gingerbread and I have been looking for a healthier (more Paleoish) recipe to make this holiday season and now I don’t have to look anymore! I can’t wait to make these!!

    Also, I’m glad I found your blog. Your recipes and pictures all look so amazing!

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  14. Ruta

    I want those. Like, now. Who cares if it’s past Christmas.

    Really, those look incredible, and I’m dying to try them, or at least some variationl. I even have a handy dandy new Silpat Baking Mat to use. Just one question for you: What would be a (nut free) substitute for the almond flour? There’s a nut allergy at my house.


    1. Running to the Kitchen Post author

      I’m honestly not sure about a nut free sub in these as they were created around the almond flour. You could probably just do all spelt or even all purpose flour but you might have to play with the liquids since they absorb differently than the nut flours. It’s not going to be a 1 for 1 sub.

  15. Anya

    These cookies are the best I’ve ever tried! I’ve made them twice already and I just can’t get enough. I always double the ingredients and finish all the cookies in no time. They turn out really moist and soft.
    A suggestion:
    I found it very difficult to mix the molasses, honey, coconut butter and eggs together the first time. So the second time I melted the ingredients (except eggs) together in the microwave (for abou 45 seconds) and then mixed in eggs using a hand blender.
    Also I found that it’s better to have the chocolate chopped very coarsely, into big chunks. Then when you eat them warm the chocolate practically drips out of them…
    And something about the sugar coating gives them a very nice shape and preserves all the softness inside.
    Love ’em!

  16. Amanda

    I have no idea what I did wrong….but mine turned out like flat, black pancakes! although they taste really good – I was hoping for the “cookie” effect for some ‘kid appeal’ with my son . What did I do wrong?…obviously nobody else had the same issue. Ok, I didn’t melt the coconut oil because I was being lazy – could that really have caused the flat-pancake effect?? Or different type of molasses?

    1. Gina Matsoukas Post author

      Amanda- yes, melting the coconut oil makes a big difference b/c if it’s not melted it won’t distribute through the batter. You’ll have chunks of oil spots that would result in flat cookies once they hit the heat in the oven and melt. I’m not sure if you made any other substitutions, but if so, they could’ve contributed as well.

  17. Amanda

    Thanks for the quick response!! Yes…then not melting the coconut oil did it!
    Thankfully everyone still likes them – next time, I’ll make them properly : )

  18. Deanna

    HaHA!! I’m glad I read all the comments…I’m another one who didn’t melt the coconut oil beforehand, just stirred it in *until* it was melted and smooth with the other wet ingredients. With *my* little lazy slip-up, I got gigantic, flat, chewy cookies that needed to be cooked an additional 8 minutes, but they are TO DIE FOR! I will probably make them this way again, only separate them into 24 cookies on two pans.
    I LOVE THESE COOKIES! Thanks for the wonderful recipe :-D!

  19. Erin

    These turned out so great. I followed the recipe exactly, except I used coconut sugar to roll the dough in before baking. They were a big hit with my crossfit gym, and even a non-paleo coworker. Thank you!

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  21. Shelley

    Hi Gina,
    These cookies look fantastic and I can’t wait to bake them. Just one question though. I want to make them gluten free and wondering what I could use instead of the spelt flour? Should I replace with more almond meal or perhaps use brown rice flour?

    1. Running to the Kitchen Post author

      Shelley- last paragraph of the post addresses this. I haven’t made them with all almond, but I’m betting it would be an ok sub. let me know how they turn out if you try it.

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  35. Heather

    I made these with whole wheat flour since I was out of spelt. AMAZING. If you’re considering a recipe. This one is perfect.

  36. Lucy

    Dough tasted great, added 2x the ginger and subbed in a gf flour blend for spelt. Seem to be holding shape well in oven + sure they will taste great.

  37. sbrnyc752

    YAY for a gingerbread cookie that doesn’t call for sticks of butter or 25 different spices I don’t have–this is a rarity among these cookie recipes! I added some chopped crystallized ginger because I love the added texture and spice, but otherwise made is written and YUM! Thank you.


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