Healthy miso cookies with apple chunks that are gluten-free, oil-free, and refined sugar-free. A wholesome Japanese twist with sweet umami flavor!
Should I call this a scone or a cookie? I’m not sure, and honestly, I don’t care because it tastes so good either way 🙂
I’ve been obsessed with these healthy miso cookies lately. They’ve become my go-to for breakfast or a mid-afternoon snack with tea.
I still love a traditional Japanese breakfast with rice, miso soup, and natto, but some mornings just call for something quick, cozy, and a little sweet. That’s where these cookies come in. The natural sweetness of apples pairs beautifully with the savory depth of miso, creating that perfect umami-meets-dessert balance.
If you enjoy this kind of healthy Japanese-inspired snack, try my brown butter matcha chocolate chip cookies or Japanese sweet potato dessert.
Watch How to Make Healthy Apple Miso Cookies
Why You'll Love This Recipe
- Gluten-free, oil-free, and refined sugar-free: I challenged myself to make cookies that are wholesome and healthy enough to enjoy every morning, and here we have them! These are gentle on the stomach and still delicious. They’re not chewy like traditional cookies (to be honest) and more like a scone-ish texture, but they taste just as good in their own way.
- Vegan and vegetarian friendly: This recipe doesn’t use any animal products, so my vegan and vegetarian friends can enjoy it too.
- Easy and simple: You don’t need any fancy techniques or tools. Just mix everything together, bake, and you’re done!
- Perfect sweet and savory balance: The mild sweetness from natural ingredients pairs beautifully with the gentle saltiness of miso. It creates a unique, umami-rich flavor that’s far more satisfying than simply combining sugar and salt.
Notes on Ingredients
See the recipe card for the full ingredients list.
- Oat flour: Use certified gluten-free oat flour.
- Coconut flour: Adds a rich nuttiness and helps absorb moisture. Since coconut flour absorbs much more liquid than other gluten-free flour alternatives, it can’t be substituted.
- Peanut butter: Chunky peanut butter gives the cookies a nice texture and richness. Use one that doesn’t contain added sugar.
- Unsweetened applesauce: Adds moisture and natural sweetness. Choose an unsweetened variety with no added sugar.
- Miso: You can use any type of miso, but keep in mind that red miso is saltier than white or mild miso.
- Maple syrup: Use pure maple syrup for the best flavor.
💡You can find these ingredients at Japanese or Asian grocery stores, or online at Amazon or Weee!
How to Make Healthy Apple Miso Cookies
- Microwave cubed apples with cinnamon and water, then chill.
- Measure and freeze peanut butter to firm up.
- Mix wet ingredients in one bowl and dry ingredients in another.
- Cut in chilled peanut butter with a fork.
- Add wet mixture, stir, then fold in apples.
- Scoop dough onto a baking sheet and flatten tops with a fork.
- Bake at 400°F for 15 min.
- Transfer them to a cooling rack and let them cool for 10 minutes.
Kurumi's Tips
- Microwave the apples thoroughly: Microwave until there’s little to no liquid left in the bowl, about 6-7 minutes.
- Adjust the amount of maple syrup: The cookies turn out softer and more moist with 3 tablespoons of maple syrup, but I usually stick with 2 because they’re sweet enough for me and still have a great texture. If you like a sweeter cookie or want the best texture, go with 3 tablespoons; otherwise, 2 tablespoons will do the job perfectly!
- Don’t worry about overmixing: Since this is a gluten-free recipe, you don’t need to worry about gluten development. Just enjoy mixing the dough without overthinking.
Storage & Reheating Instructions
- To store: Once completely cool, place the cookies in an airtight container. Keep at room temperature for 2–3 days, in the fridge for up to 1 week, or in the freezer for up to 2 months.
- To reheat: I like to crisp up the outside by warming them in an air fryer at 400°F for about 3 minutes. You can also gently warm them in the oven if you prefer.
FAQs
Can I replace the coconut flour with something else?
No, because coconut flour absorbs much more moisture than other gluten-free flours like almond flour, it can’t be substituted.
More Recipes with Miso
Looking for other recipes like this? Try these:
💌 If you tried this recipe and liked it, I’d love to hear from you! Leave a comment and review below or send a photo of your dish to my email. I’d be so happy to see your creation!
📖Recipe
Healthy Apple Miso Cookies (Gluten-Free, Oil-Free & Refined Sugar-Free)
Healthy miso cookies with apple chunks that are gluten-free, oil-free, and refined sugar-free. A wholesome Japanese twist with sweet umami flavor!
Ingredients
Method
- Prep the apples: Cut the apples into 0.5 cm (0.2 inch) cubes. Toss them with a little water and cinnamon in a microwave-safe bowl. Cover loosely and microwave for about 6-7 minutes, or until there’s little to no liquid left. Remove the cover and let the apples cool in the fridge until you need them.2 small apples, 2 tablespoons water, 1 teaspoon cinnamon powder
- Prep the peanut butter: Measure the peanut butter in a small bowl and chill it in the freezer until you need it.¼ cup chunky peanut butter
- Prep for baking: Preheat the oven to 400°F. Line a large baking sheet with parchment paper.
- Mix the wet ingredients: In a medium bowl, combine the applesauce, maple syrup, and miso.½ cup unsweetened applesauce, 2-3 tablespoons pure maple syrup, 1 tablespoon miso
- Mix the dry ingredients: In a large bowl, whisk together the oat flour, coconut flour, and baking powder.1 cup oat flour, 3 tablespoons coconut flour, 1 teaspoon baking powder
- Add the peanut butter: Add the chilled peanut butter to the dry ingredients. Use a fork to “cut it in” — this means breaking the peanut butter into small pieces and mixing it lightly with the flour so it’s evenly distributed, but not fully blended. You’ll see little bits of peanut butter throughout, which makes the cookies crispy and tender.
- Combine wet and dry: Pour the wet ingredients into the large bowl with the dry mixture. Mix with a spatula until the flour is fully moistened.
- Add the apples: Fold in the cooled apple cubes until everything is evenly combined.
- Scoop the cookies: Use a #20 cookie scoop to portion 10 cookies onto the prepared baking sheet. Flatten the tops gently with a fork so each cookie is about 1 cm (0.4 inch) thick.
- Bake: Bake for 15 minutes at 400°F or until the tops turn golden brown.
- Cool and enjoy: Transfer the cookies to a cooling rack and let them cool for about 10 minutes before enjoying.
Notes
- (Note 1) The amount of maple syrup: The cookies turn out softer and more moist with 3 tablespoons of maple syrup, but I usually stick with 2 because they’re sweet enough for me and still have a great texture. If you like a sweeter cookie or want the best texture, go with 3 tablespoons; otherwise, 2 tablespoons will do the job perfectly!
- Ingredients
- Oat flour: Use certified gluten-free.
- Coconut flour: Adds nuttiness and absorbs moisture; can’t be substituted.
- Peanut butter: Use chunky, no added sugar for texture and richness.
- Applesauce: Unsweetened, adds moisture and natural sweetness.
- Miso: Any type works; red miso is saltier.
- Maple syrup: Use pure for best flavor.
- Storage & Reheating: Once cooled, store in an airtight container: room temp 2–3 days, fridge 1 week, freezer 2 months. Reheat in an air fryer at 400°F for ~3 minutes.
- Other Japanese-inspired sweets: Try my brown butter matcha chocolate chip cookies or Japanese sweet potato dessert for more delicious treats!
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Kurumi says
I love these cookies so much that I didn’t even mind testing them over and over (um… like 17 times). I happily ate every batch! They’re also a great go-to snack, and my husband can just grab a few for breakfast or for a quick bite at the office. I hope you give them a try and love them too!