Whole Wheat Chocolate Fudge Cookies

Thick, fudgy, and rich, these whole wheat chocolate fudge cookies are a chocolate lover’s dream come true.

A whole wheat chocolate fudge cookie with a bite taken out of it next to more cookies and chocolate chips.

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Would you believe me if I told you that this cookie recipe gets more compliments than any other dessert I make? That’s right, a cookie recipe using whole wheat flour is my claim to fame.

This recipe is a result of an intense craving for a big, puffy chocolate cookie, and poor planning. I have been obsessed with these cookies ever since Lindsay blogged about them, so naturally, I decided to make them immediately.

Problem was, I had already melted my butter when I realized I was out of white flour. I decided to do the unthinkable – replace the white flour entirely with whole wheat flour. I know that whole wheat flour can make baked goods a little dry, so I decreased the overall amount of flour and used brown sugar to pump up the moisture.

The result? Big, puffy, cookies with the perfect fudgy texture and decadent chocolate taste.

Ingredients

Butter
Granulated sugar
Dark brown sugar
Vanilla extract
Eggs
Unsweetened cocoa powder
Whole wheat flour
Baking soda
Salt
Semisweet Chocolate Chips

How to make whole wheat chocolate fudge cookies

Place one stick of butter on the kitchen counter to soften. Place the other stick of butter in a microwave safe bowl and melt completely in the microwave. Allow the butter to cool to a semisoft texture either on the counter or in the refrigerator.
Cream the softened butter, microwaved butter, and both sugars until fluffy. Add vanilla and eggs and mix briefly until just incorporated.
In a separate bowl, whisk together cocoa powder, flour, baking soda, and salt. Add the flour mixture to the butter mixture and combine. Stir in chocolate chips.
Cover the top of the bowl tightly with plastic wrap and allow the dough to rest in the refrigerator for 30 minutes or up to 2 days.
When you’re ready to bake the cookies, preheat the oven to 350ºF. Roll the dough into balls slightly larger than a golf ball and place two inches apart on a baking sheet lined with parchment paper or a Silpat (affiliate link). Bake 8-9 minutes. The cookies should be puffy and soft. Allow to cool on the baking sheet for 5-10 minutes before transferring to a cooling rack to cool completely.

Whole wheat chocolate fudge cookies on a cooling rack.

Top tips

Alternatives to whole wheat flour

The wheat flour in this recipe gives it a really nice, nutty taste. However, if you don’t have wheat flour or don’t want to use it, simply swap it for white whole wheat flour, which has a finer texture and less pronounced taste.

You could also swap it for all-purpose flour, but would need to increase the amount to 2 ⅔ cups of flour since wheat flour absorbs more liquid.

The best whole wheat flour for baking

I love North Dakota Mill‘s whole wheat flour, but you may not be able to find that everywhere. King Arthur Flour is another high quality brand that is readily available at most grocery stores.

A stack of whole wheat chocolate fudge cookies.

How to know when your cookies are done

This recipe is best baked by time, rather than sight. The cookies will still appear underbaked on the top when you pull them out of the oven, but should solidify as they cool.

Since all ovens are different, bake your first batch for 8 minutes, allow them to cool, and then adjust the baking time as needed for future batches. You want your cookies to be soft but still hold together when you pick them up after cooling.

How to store whole wheat chocolate fudge cookies

Allow your cookies to cool completely, then store at room temperature in an airtight container for up to 4 days. They stay surprisingly soft for a cookie! Cookies can also be frozen in a freezer zip top bag for up to 6 months.

Tips for customizing

Swap the chocolate chips for dark chocolate, white chocolate, peanut butter, or any favorite combination of baking chips
Skip the chilling for a flatter cookie
Swap the wheat flour for white flour, increasing the amount to 2 ⅔ cups
Bake into bars. I haven’t tested this, but would guess that in a 9×13 pan you should test for doneness around 25 minutes.

FAQ

Is it necessary to chill cookie dough before baking?

Chilling cookie dough before baking is an optional step that will improve both the flavor and texture of your finished cookie. Specifically, that is what gives this cookie a little height and a “puffier” texture.

If you prefer, or time does not allow for chilling, you can skip this step.

Why melt half the butter?

Melting half the butter creates a specific texture when mixing the cookie dough that I find irresistible. If you prefer to melt all the butter, or work with all softened butter, you will still get a delicious cookie, just with a slightly different texture.

Should I use salted or unsalted butter for cookies?

Most bakers swear by unsalted butter for baking cookies. I don’t usually have unsalted butter on hand and usually use salted.

You can use either, just keep in mind that if you use unsalted butter you’ll want to add some salt to the dough yourself (up to 1 teaspoon), and if you use salted butter you will only need to add a pinch or maybe none at all.

Whole wheat chocolate fudge cookies on parchment paper next to chocolate chips.

More cookie recipes

A whole wheat chocolate fudge cookie broken in half.

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4.12 from 60 votes (50 ratings without comment)