This cleaned up, healthier Moon Pie recipe is gluten free, refined sugar free, and totally delicious! If you’re looking for a better way to enjoy these classic snack cakes, then this is the recipe you’ve been searching for.

WHY I MADE THESE HOMEMADE MOON PIES

When I first started sharing my healthier homemade recipes online, the first recipes I tackled were copycats of my favorite store bought snacks and desserts. Because I’m just a girl, and I love a chocolate snack cake as much as the next girl, but I don’t necessarily want to indulge in all of the over-the-top ingredients that often accompany most mass produced desserts.

Moon Pies, for those who don’t know, are a classic, Southern chocolate snack cake that consists of marshmallow fluff sandwiched between two graham cracker cookies, and dipped in chocolate. Yum, right? They’re just as good as they sound.

And because it’s summer, I couldn’t help but think about how Moon Pies are basically Southern s’mores. So this time of year seemed like the purrfect time to share my healthy homemade Moon Pies recipe with you all!

GLUTEN FREE MOON PIES KEY INGREDIENTS

I made this healthy Moon Pies recipe because I love snack cakes as much as the next girl, but I don’t love the weird ingredients that are included in most store bought desserts. That’s the main reason why I started this blog in the first place: so that I could indulge in the foods that I love while still maintaining the wellness principles that are so important to me.

So, I’m proud to say that this homemade Moon Pie recipe is made with clean ingredients that you’re already familiar with! Not only is this summer dessert recipe gluten free, it can also be made refined sugar free with a few simple tweaks.

No, this isn’t a keto, sugar free, Whole 30, paleo, etc., etc., etc. alternative to traditional Moon Pies. This is a dessert, and should be categorized as such.

But if you’re someone who likes to indulge and also likes to know exactly what they’re eating and wants to feel good about it too, then I’m glad you’re here! This recipe is 100% for you.

Gluten Free Graham Crackers

• Almond flour
• Arrowroot flour (or Cornstarch)
• Coconut sugar
• Cinnamon
• Egg 
• Coconut oil 

Honey Marshmallows (or, use store bought marshmallow fluff)

• Gelatin
• Honey
• Vanilla

Chocolate Coating

• Chocolate chips (use dairy free or refined sugar free, if desired)
• Coconut oil

MY HEALTHIER CHOCOLATE MOON PIE RECIPE

You may look at this recipe and think that it’s too many steps, and I get that. This recipe is definitely not for people who don’t enjoy being in the kitchen, especially if you go the route of making your own marshmallow fluff, which is what I did.

But, the easiest way to cut down the active time for this Moon Pie recipe is to use store bought marshmallow fluff. I prefer to make my own using my Homemade Honey Marshmallows because store bought marshmallow fluff tends to have lots of sugar and weird ingredients in it, but there are a few cleaner alternatives on the market now, like this one from the brand Choc Zero which is both Keto and Gluten Free!

Still, here’s an overview of how to make everything:

Gluten Free Graham Crackers

• In a large bowl, mix together the almond flour, arrowroot flour, coconut sugar, cinnamon, and salt.
• Scoop the coconut oil and egg into the well. Mix together until a dough forms.
• Use a rolling pin to roll out the cookie dough until it’s about 1/4″ thick. Don’t make them too thin, or else they will break.
• Use a round cookie cutter to stamp out the cookies. You should have at least 10 cookies total.
• Bake for 15 minutes, rotating the baking sheets halfway through.

Homemade Marshmallow Fluff

• Pour 1/4 c hot water and the gelatin into the bowl of stand mixer, stirring them together until the gelatin dissolves.
• In a medium pan over medium heat, combine another 1/4 c water, honey, vanilla, and pinch of salt. Stir together briefly, and let the mixture simmer.
• Simmer the mixture until it reaches 240F.
• Slowly pour the sugar mixture into the stand mixer, being careful not to splash it. Whip the mixture for about 10 minutes, until soft peaks form. The marshmallow will be thick and delicious.

Chocolate Coating

• Melt the dark chocolate chips and coconut oil until the chocolate is very smooth.

Assembly

• Dollop marshmallow fluff on half of the graham cracker cookies. Work quickly, as the fluff will harden the longer it sits out, making it harder to spread. Top with the remaining cookies to create a marshmallow cookie sandwich.
• Dip the cookie sandwich in the melted chocolate. Repeat with the remaining sandwich cookies.

HOW LONG DO THESE CLEAN MOON PIES TAKE TO MAKE?

This recipe does take a little bit of time to make, but it’s not terrible (I promise)! Rolling out and cutting out the cookies is probably the most time consuming part of this homemade Moon Pie adventure. I don’t particularly love rolling out and cutting out cookie dough, either, but trust me it’s worth it once you get to taste these delicious homemade Moon Pies!

In total, it will take you about 1 hour to make these Moon Pies. That assumes that you’re doing a bit of multitasking. If you’re not a multitasker in the kitchen, though, then tack on about 30 extra minutes to get a more accurate timeline for making this recipe.

But, in general, here’s about how long it will take to make these Moon Pies:

• Prep time: 35 mins
• Bake time: 25 minutes
• Total time: 1 hour

HOW TO STORE THESE HOMEMADE MOONPIES?

If you have any leftover homemade Moon Pies, place them in an airtight container in the fridge and they will stay fresh and delicious for about 5 days.

Honestly, I think these taste even better straight out of the fridge! Something about a cold Moon Pie on a hot summer day… yum.

CLEAN MOON PIES FAQ

1. Are these MoonPies actually healthy?

Compared to store-bought MoonPies, they’re definitely a better option! These are made with whole food ingredients including almond flour, coconut oil, natural sweeteners like honey or maple syrup, and dark chocolate. They’re also gluten-free and can be made refined sugar-free and dairy-free, depending on your ingredients.

That makes them “healthy” to me, but your definition may be different. Either way, I know you’ll enjoy this recipe!

2. Can I make these MoonPies vegan?

Yes, with a few tweaks:

• Use vegan gelatin for the marshmallow.
• Choose maple syrup or agave instead of honey.
• Make sure your dark chocolate is dairy-free.

3. Are these gluten-free?

Yes! The graham crackers are made from almond flour and arrowroot flour, making them 100% gluten-free. Just be sure to check all other ingredients (like chocolate chips) to ensure they’re certified gluten-free if needed.

4. What’s a good substitute for arrowroot flour?

You can use cornstarch in the same amount. Tapioca starch may also work, though the texture might be slightly chewier.

5. Can I use store-bought marshmallow fluff instead of making my own?

Absolutely. If you’re short on time, store-bought marshmallows (or marshmallow fluff) work. For a cleaner option, look for ones with natural ingredients and no high-fructose corn syrup, like this one from Choc Zero.

6. How do I store them?

Keep your finished MoonPies in an airtight container in the fridge for up to 5 days. You can also freeze them (individually wrapped) for up to 3 months.

7. Why did my marshmallow fluff harden so quickly?

Homemade marshmallow begins to set as it cools, so it’s best to assemble the Moon Pies quickly. If it starts to firm up, you can try whisking it briefly to loosen it again, or reheat gently in a warm bowl.

8. What kind of chocolate should I use?

Go for dark chocolate chips (60–70% cacao) for a richer, less sweet finish. Look for ones with minimal ingredients and no dairy if you’re keeping it vegan.

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If you love this recipe be sure to leave a review! And feel free to reach out to me with any questions or comments via my Contact page. You’ll hear back from me soon!

Find even more of my homemade recipes on Instagram, TikTok, Pinterest, and YouTube.

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Gluten Free MoonPies

This cleaned up, healthier Moon Pie recipe is gluten free, refined sugar free, and totally delicious! If you're looking for a better way to enjoy these classic snack cakes, then this is the recipe for you.

Print Pin Rate

Course: Dessert

Prep Time: 35 minutes minutes

Cook Time: 25 minutes minutes

Total Time: 1 hour hour

Servings: 5 sandwiches

Equipment

• GF/RSF Marshmallow Fluff optional
• Candy Thermometer
• Rolling Pin

Ingredients

Gluten Free Graham Crackers

• 2 c almond flour
• 1/2 c arrowroot flour or cornstarch
• 2 tbsp coconut sugar
• 1 tsp cinnamon
• 1 egg beaten
• 6 tbsp coconut oil softened
• Pinch of salt

Honey Marshmallows (Or, use store bought)

• 1/2 c water divided
• 1 tbsp unflavored gelatin or: vegan gelatin if vegan
• 1/2 c honey or: maple syrup or agave syrup, if vegan
• 2 tsp vanilla extract
• Pinch of salt

Chocolate Coating

• 10 oz dark chocolate chips use dairy free or refined sugar free, if preferred
• 1 tsp coconut oil

Instructions

Gluten Free Graham Crackers

• Preheat oven to 350 F. Gather two baking sheets, and a roll of parchment paper. Set aside for now.
• In a large bowl, mix together the almond flour, arrowroot flour, coconut sugar, cinnamon, and salt.
• Make a well in the center of the flour mixture, and scoop the coconut oil and egg into the well. Mix together until a dough forms. You may want to use your hands at the end.
• Lay a sheet of parchment paper on the counter, and place the cookie dough ball in the middle. Top with another sheet of parchment paper, and use a rolling pin to roll out the cookie dough until it's about 1/4" thick. Make sure not to make them too thin, otherwise they may break during assembly.

  Remove the top sheet of parchment paper.
• Use a round cookie cutter (mine is 4" wide) to stamp out the cookies.
• Remove the excess dough from the cookies, and roll the extra dough out again to make more cookies. You should have at least 10 cookies total. Divide the cookies between both baking sheets, spacing them apart. The cookies will not spread, but they should not be touching.
• Bake for 15 minutes, rotating the baking sheets halfway through, until the cookies are just lightly brown.
• Remove from the oven and cool completely before using.

Homemade Marshmallow Fluff

• Fit a stand mixer with the whisk attachment. Pour in 1/4 c hot water and the gelatin, stirring them together until the gelatin dissolves.
• In a medium pan over medium heat, combine another 1/4 c water, honey, vanilla, and pinch of salt. Stir together briefly, and let the mixture simmer. Clip your candy thermometer to the side of the pan, making sure the bottom is submerged in the liquid so it can accurately read the temperature.
• Simmer the mixture until it reaches 240F. You can turn up the heat to medium-high or high if you need to, but do this gradually so that the mixture does not pass 240F. Immediately remove the pan from heat when this happens.
• Turn the stand mixer to medium-high, and slowly pour the sugar mixture into the stand mixer, being careful not to splash it. Whip the mixture for about 10 minutes, until soft peaks form. The marshmallow fluff will be thick and delicious.

Chocolate Coating

• Pour the dark chocolate chips and coconut oil into a microwave-safe bowl. Microwave at 15 second intervals, stopping to stir each time, until the chocolate is very smooth.

Assembly

• Line a baking sheet with parchment paper and place it on your counter.
• Gather your ingredients: the graham cracker cookies, marshmallow fluff, and melted chocolate.
• Dollop a big spoonful of marshmallow fluff on half of the graham cracker cookies, lightly spreading the fluff to the edges of the cookie. Top with the remaining cookies to create a marshmallow cookie sandwich.

  Work quickly, as the fluff will harden the longer it sits out, making it harder to spread. Handle the cookies carefully so they don't break.
• Working one at a time, dip the cookie sandwiches in the melted chocolate, rolling the edges in the chocolate first, and then laying the cookie flat in the pool of chocolate.

  Use a spoon to drizzle more chocolate on top of the cookie to coat. Use a fork to scoop the coated sandwich cookie out of the chocolate, allowing any excess to drip off, and then place it on the baking sheet. Repeat with the remaining sandwich cookies.
• Place the MoonPies in the fridge until the chocolate is set, about 15 minutes. Enjoy!