Learn how to make Healthy Molasses Cookies that are soft, chewy, and delicious!

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Healthy Molasses Cookies

These deliciously soft and chewy cookies already have a good bit of nutrition, thanks to the wonderful addition of molasses. We further increase this cookie recipe’s healthiness by using whole grain flour and honey in place of white flour and refined sugars.

Choose the Flour for Your Molasses Cookies

Depending on where you are on your journey from processed foods to traditional foods, you can make these molasses cookies with whole wheat flour. However, if you have already started incorporating ancient grains into your baking, you can switch to making these cookies with Einkorn or Spelt flour.

If you’re new to using Einkorn in baking, check out the All About Einkorn Flour video where I share everything you need to know about this original ancient grain.

If you have branched out into baking with sprouted flours, these flours are perfect for this recipe too. You may be buying your sprouted flour right now, but if you would like to learn how to make your own sprouted flour, be sure to watch the How to Make Sprouted Flour video. I walk you through the whole process, step by step.

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Make Your Own Baking Ingredients

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More Delicious Desserts

With Christmas just around the corner, you may enjoy making some of these wonderful sweet treats:

Last Minute DIY Gifts

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Healthy Molasses Cookies

5 from 6 votes
Prep: 5 minutes
Cook: 10 minutes
Chilling Time: 4 hours
Total: 4 hours 15 minutes
Yield: 36 cookies
These cookies are a healthy sweet treat thanks to the addition of whole wheat flour and honey.


  • Half-sheet sized baking sheet
  • Parchment paper, optional


  • 2 cups Whole wheat flour or whole grain flour Sprouted flour may also be used.
  • 1 tsp Baking soda
  • 1 tsp Ground cinnamon
  • 1 tsp Ground cloves
  • 1 tsp Ground ginger
  • 1 tsp Ground allspice, optional
  • 1/2 tsp Salt
  • 1 stick Butter, softened 1 stick butter = 1/2 cup butter
  • 3/4 cup Honey or maple syrup If you want to use a dry sweetener, such as Sucanat, coconut sugar, maple sugar, or date sugar, increase the amount to 1 cup.
  • 1/4 cup Molasses
  • 2 large Eggs
  • 1 cup Coarse sugar such as turbinado If you do not have a coarse sugar, you can substitute it with regular sugar.


  • Into a mesh strainer over a medium bowl, add flour, baking soda, all the spices, and salt. Shake everything through the strainer into the bowl. Set aside.
  • In a separate large bowl, cream together the butter, honey, and molasses until creamy and smooth, about 2-3 minutes.
  • Add the eggs to the butter mixture, one at a time, and beat till incorporated, about 30 seconds.
  • Add the flour mixture to the butter mixture and mix until combined and no streaks or flour are visible.
  • Cover the bowl with plastic wrap and chill the dough for at least 4 hours or overnight.
  • Once the dough is well chilled and firm to the touch, Preheat the oven to 375°F and line a baking sheet with parchment paper. (If you do not have parchment paper, grease the baking sheet with butter.)
  • Place the turbinado or other sugar in a small bowl.
  • Roll a teaspoon full of cookie dough between the palm of your hands until it forms a 1-inch ball. Next, roll the cookie dough ball in the sugar and place the ball onto the baking sheet. (See video.)
  • Continue rolling the dough into balls, rolling the balls in the sugar, and then placing the dough balls on the baking sheet until you have 12 dough balls on the baking sheet that are placed two inches apart.
  • Using a flat-bottomed glass dipped in water, flatten each dough ball to 1/4-inch.
  • Place the baking sheet on the middle rack of your preheated oven and bake the cookies until they crack on top, approximately 8-10 minutes.
  • When done, remove the baking sheet from the oven and allow the cookies to cool for a minute or two before transferring them to a wire cooling rack to cool completely.
  • Store the cookies in an airtight container. At room temperature, the cookies will stay fresh for about one week. Refrigerated, the cookies will stay fresh for about two weeks.



Find this recipe and video at https://marysnest.com/how-to-make-healthy-molasses-cookies/
Copyright © 2020 Mary’s Nest, LLC, All Rights Reserved
Course: Cookies, Dessert
Cuisine: Americana
Keyword: Healthy Molasses Cookies, Molasses Cookies
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  1. Hi Mary!
    Your instructions for dry sugar say increase to 1/2 cup. 1/2 is less than 3/4. Is it 1/2 cup more or typo? Thank you.

    1. Hi Neha,

      Thanks for your comment. Great catch! I accidentally mistyped, and I meant to say that if you want to use a dry sweetener, you can increase the amount to 1 cup. I updated the recipe to reflect the change.

      Thanks again for letting me know. 🙂

      Love and God bless,

  2. 5 stars
    These are delicious cookies. Everyone who ate the loved them. I made these for the 2nd time today for Christmas gifts.

    1. Hi Dora,

      Wow! That’s great. I’m so happy that you were able to make these as Christmas gifts!

      Love and God bless,

  3. 5 stars
    The molasses cookies are outstanding! I made the dough yesterday and baked a few today. Thank you for such a lovely recipe, Miss Mary!

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