Keto Zucchini Bread Whoopie Pies

by Clean Keto Lifestyle

Indulge your sweet tooth with these Keto Zucchini Bread Whoopie Pies! The zucchini bread layers are so soft and perfectly compliment the tangy cream cheese frosting inside. They are keto, low-carb, grain-free, and gluten-free!

Clean Keto Zucchini Bread Whoopie Pies

Whoopie Pies – The Original Sandwich Cookie

Whoopie pies are amazing. They are basically cookies with filling inside. You know, what OREOs want to be when they grow up.

And these zucchini bread whoopie pies are the best version!

You don't need a glass of milk with whoopie pies. They are delicate and chewy and fall apart in your mouth. Oh, they are so good.

And these are keto-friendly! Read on to learn how to make these low-carb whoopie pies that you don't have to feel guilty about eating.

Clean Keto Zucchini Bread Whoopie Pies

How to Make Zucchini Bread Whoopie Pies

These are pretty simple to make. You just have to bake zucchini bread cookies.

Then, whip up some keto cream cheese frosting. Fill the cookies with the frosting.

And then, try not to eat the entire batch at once. It's tough, we know!

The entire recipe is at the bottom of the post. First, we have some helpful tips and instructions. Follow along as you make them.

Clean Keto Zucchini Bread Whoopie Pies

Main Ingredients in Keto Zucchini Whoopie Pies

First things things first, gather all of your ingredients and measure them out.

You will probably have most of the ingredients on hand in your pantry or fridge.

Here is a quick list of what you need:

Pantry Items

Fridge Items

  • Butter
  • Cream cheese
  • Eggs
  • Sour cream
  • Zucchini

How To Shred Zucchini Noodles

This recipe calls for shredded zucchini, so let's break down the basics.

You don't need to peel the zucchini before you shred it. But you should cut off both ends of the zucchini.

Either use a food processor or shred them using a handheld grater. Both options work.

  • Food Processor: Add the grating attachment to your food processor. Cut your zucchini into several smaller pieces for easier grating. Turn on the food processor and place the zucchini in the shoot of the processor to grate.
  • Handheld Grater: Place a standup box grater on a plate or cutting board on the counter and shred the zucchini by continuously running it over the large holes of the grater.

Lightly dry the shredded zucchini with paper towels.

Whoopie Pie Batter

We are going to start with the zucchini bread cookies first.

In a medium bowl, mix together the dry ingredients and in a larger bowl mix together all the wet ingredients.

Next, stir in the shredded zucchini to the wet ingredients bowl.

Slowly pour the dry ingredients into the wet ingredients and mix until combined.

If you have ever made zucchini bread before, this batter will look familiar. Since we are making cookies out of it, it won't be nearly as fluffy. It'll appear a bit denser.

It should be a nice, thick batter (like the picture below).

keto zucchini whoopie pie batter

How to Make Perfect-Sized Cookies

Take roughly 1 tablespoon of batter and form 2 inch circles on two lined baking sheets spaced 2 inches apart.

The recipe makes 16 whoopie pies, which means you need 32 zucchini bread cookies.

If you don't have two baking sheets, you can make the cookies in two batches.  The cookies only take 10 minutes to bake, so it won't add much extra time.

To keep all the cookies the same size, use an ice cream scoop. It's important to keep them the same size so they all cook at the same time (you don't want any to burn while others are still gooey).

Plus, if they are the same size, they will make prettier whoopie pies.

Clean Keto Zucchini Bread Whoopie Pies

Add the cookies to the oven and bake at 350°F for 10 minutes or until they turn golden brown.

Clean Keto Zucchini Bread Whoopie Pies

Keto Whoopie Pie Filling

While the cookies are baking, make your filling.

All you need to do is add the ingredients to a mixing bowl and use an electric mixer to combine.

Using an electric mixer will get the filling really light and well-whipped.

This filling has a similar taste and texture to frosting, so save this recipe and reuse it on top of keto cupcakes next time.

Use a Piping Bag to Add the Frosting

Make sure the cookies are cooled off completely before adding the frosting. If you add it too soon (while they are still warm), the frosting will melt.

If you want the whoopie pies to have a pretty look to them, use a piping bag.

Don't have a piping bag? Make your own! Put the frosting in a zippered plastic bag and cut a hole in the corner.

Now you are ready to squeeze the frosting onto the cookies.

Keto zucchini cookies on a cookie sheet

Pipe about 2 tablespoons of frosting on the bottom zucchini bread cookie layer.

Add another zucchini cookie on top and gently press down so that the frosting spreads almost to the edge of the cookie layers.Clean Keto Zucchini Bread Whoopie Pies

How Many Net Carbs Are in Zucchini Bread Whoopie Pies?

There are about 2.5 net carbs in each cookie. That's it!

So you really could eat a few of these at a sitting without hurting your macros.

Since these are so low in carbs, you can enjoy them as a keto-friendly breakfast.

Take them to your next party or serve them at a weekend brunch. They present beautifully.

Clean Keto Zucchini Bread Whoopie Pies

Are These Keto Whoopie Pies Good for You?

Actually, they are pretty nutritious. Normally, whoopie pies are full of sugars and refined grains.

But our Clean Keto version is low-carb, grain-free, and full of vitamins, so eat up.

They are a fantastic source of healthy fats and protein.

Plus, the shredded zucchini contains significant amounts of Vitamin B6, riboflavin, folate, Vitamin C, Vitamin K, potassium, and manganese.
Clean Keto Zucchini Bread Whoopie Pies

Can You Leave Out the Shredded Zucchini?

This recipe is really easy to modify. If you don't like zucchini or don't have any on hand, you can leave it out completely. It won't change the cookies that much.

Or, you can replace the zucchini with shredded carrots. That will add some color to it. Just make sure the carrots are shredded very thin since they have a different texture.

Also, carrots have a higher carb count, so the macros will change a little.

Clean Keto Zucchini Bread Whoopie Pies


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Leave a Comment


Suzanne September 18, 2019 - 2:40 pm

These look so good! Do you use this dough base for any other recipes?

Clean Keto Lifestyle September 18, 2019 - 8:50 pm

Hi Suzanne,

We use the same dough for regular zucchini bread. To make 2 whole loaves, just double the recipe (except only use 3 eggs) and bake in two 8″x4″ loaf pans at 325°F for 40-55 minutes.


Debbie September 18, 2019 - 7:53 pm

I would like to make these without the artificial sweetener, for my grandson what would be the measured substitution of sugar/ coconut sugar .? Would it be the same 1:1 substitution? They look so yummy!

Clean Keto Lifestyle September 18, 2019 - 8:26 pm

Hi Debbie! They are so delicious! Yes – substitute the erythritol 1:1 for regular or coconut sugar.

emily September 18, 2019 - 7:54 pm

Just wondering how to store these Whoopie pies, and do they freeze well?

Clean Keto Lifestyle September 18, 2019 - 8:24 pm

Hi Emily!! Store any leftover Whoopie Pies in a sealed container in the fridge. In terms of freezing them, we would recommend only freezing the baked zucchini bread layers. Then just whip up a batch of the cream cheese filling when you are defrosting the layers.

Bridget September 19, 2019 - 9:46 am

Would this recipe still work if I double it?

Clean Keto Lifestyle September 19, 2019 - 6:55 pm

Hi Bridget!! Absolutely! Just make to stir all the ingredients really well!

Maria September 20, 2019 - 2:36 pm

How about substituting zucchini with pumpkin puree? Would this work? I love zucchini bit I have pumpkin puree on hand at the moment.

Clean Keto Lifestyle September 20, 2019 - 3:03 pm

Hi Maria! We *think* this substitution will work. We would recommend baking a small test batch of the whoopie pie layers first. Also, the baking times may need to be adjusted slightly as well. Keep us posted on how they turn out!

Maria October 9, 2019 - 8:25 pm

These things are amazing!!!! I was going to try them with pumpkin puree a few weeks ago but ended up using it on something else…I just made these and I cannot believe how good they are. I did have to put in 1/2 extra of flour and they took about twenty minutes to bake. I also reduced the sugar by 1/3 on the frosting

Clean Keto Lifestyle October 10, 2019 - 12:11 pm

Yay!!! So glad you loved them!!!

Jennifer September 21, 2019 - 2:33 pm

I made these last night for the first time. AMAZING!! My husband and father are doing low carb and have been craving a dessert for several weeks. I am so glad I found your recipe. I used the Swerve brand substitute as you mentioned above. No weird aftertaste! This was a huge hit and will be a routine treat for us. Thank you for sharing recipe with everyone. Next time I will try it as a zucchini loaf.

Clean Keto Lifestyle September 22, 2019 - 12:39 pm

Hi Jennifer!! Yay – we are so glad they were a hit!!! Thanks so much for letting us know!

Hyun September 25, 2019 - 6:42 pm

This recipe looks amazing! Just wondering, would it be okay to substitute butter for coconut oil?

Clean Keto Lifestyle September 25, 2019 - 9:19 pm

Hi Hyun!! Yes – you should be able to substitute butter for coconut oil.

Cherie November 8, 2019 - 7:41 pm

These were amazing! My husband and I are doing keto and are always wanting some treat! This fits perfectly! I also had to cook them 20 mins. Thanks for sharing!

Clean Keto Lifestyle November 8, 2019 - 8:34 pm

Yay!!! So glad you liked them!! Thanks so much for your kind words!



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