Healthy Apple Cobbler Muffins (With Easy, Make-Ahead Tips!)

~ Comforting, delicious apple cobbler in a portable muffin! Bursting with apple flavor under a decadently crunchy cobbler topping. Really healthy and freezes great! ~

This Recipe Is:     Freezable    Make Ahead    Vegetarian  

THK Apple Cobbler Muffin7

Apple cobbler. *Sigh*  So warm and comforting. Like fall is wrapping you in a giant bear hug.

But apple cobbler as a grab-and-go snack? Or for breakfast as you dash out the door on a busy morning? Unheard of! (That’d be one super-sloppy bear hug!)

Enter the Apple Cobbler Muffin: Bursting with apple flavors and fall spices, then studded with a satisfying, crunchy-craggy cobbler topping.

THK Apple Cobbler Muffin5

It. Is. So. Good.

A bear hug for the uber-busy, let’s say. (And aren’t the uber-busy really the people most in need of a good bear hug, anyway!?!?)

If you know us, then you know we tested and re-tested our recipe until we found the exact right balance of apple flavors, the perfect amounts of spices, and just the right texture (as in: soft, pillowy muffin meets nutty-crisp topping … ahhhhhh …).

THK Apple Cobbler Muffin2

Plus, we jam-crammed in tons of great nutrition with whole-wheat flour and oats, protein from two eggs and those yummy walnuts, and LOADS of healthy apples. (Apple four ways, seriously – two kinds of apples, plus apple juice and apple sauce. One of these a day should keep the doctor away for eons!)

But wait … it gets even better! These really are muffins for the uber-busy, for all of you who think you don’t have time to bake homemade muffins. We’ve worked all the angles!

No need to complete the entire prep and baking process all at once! You can get everything ready the night before you’re gonna bake, or even earlier in the day. So easy! Here’s how:

  • Prepare the large bowl of dry ingredients, then wrap it in plastic and set it aside on the counter.
  • The bowl of wet ingredients … wrap and stash it in the fridge.

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  • You can even pre-shred the apples, then wrap them and store them in the fridge, too. They’ll turn a bit brown, of course, but that won’t affect the final delicious flavor a bit!

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  • Lastly, you can even toss together the cobbler topping ahead of time. For the very best results, we recommend that you don’t mix in the topping’s apple sauce and butter until you’re ready to bake the muffins. But, honestly, you really can mix the entire cobbler topping together and keep it wrapped in the fridge, too. We’ve tried it and can tell you it really turns out almost as good!

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  • When you’re ready to bake, just mix all the ingredients together! 

Oh – and the ultimate make-ahead tip? These freeze great! (So, make a double batch while you’re at it!) Once they’ve cooled completely, package them individually in plastic wrap and then seal them in freezer bags. Air is the enemy that will lead to freezer burn, so try to wrap them tightly and remove as much air as you can.

Just a couple quick tips and you’ll be ready to start:

  • As with most of our muffins, these perform beautifully when baked in foil muffin liners. Sure, you can use regular paper liners, but the muffins won’t release quite as easily, especially on the first day. For the perfect balance of non-stick style (’cause who doesn’t love a stylish muffin, right?!?!), look for patterned muffin cups that have an inner foil lining like the ones we used for photographing this post.

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  • After trying various combinations (including zucchini!), we fell in love with a mixture of half Granny Smith apple (so tart and refreshing!) and half Pink Lady (for sweetness). Use what you have on hand or what’s available at your local markets or orchards. There will be differences in flavor and texture depending on which apples you choose, but these are so good that the most important thing is just to hurry up and make them! (Now!)
  • Oh – and all that cinnamon? Yup. We monkeyed with the cinnamon and ginger (as well as cardamom and nutmeg, which didn’t make the cut!) until the flavor was exactly where we wanted it. Trust us – don’t skimp on the cinnamon!

The perfect, healthy, satisfying solution for busy-morning breakfasts and on-the-go snacks. It’s a cobbler … and it’s a big bear hug … all wrapped up in a delicious muffin …

THK Signature Gretchen & Shelley cropped

P.S. Want more yummy hugs? Check out some of our other healthy and delicious muffin recipes, like our Praline Peach Muffins or our Blueberry-While Chocolate Muffins!

We’d Love to Hear From You!

Ahhhhh … fall in Ohio. We love the weekends spent with our families in the cooler temps amid the gorgeous autumn colors! Hiking in the parks nearby, laughing our way through corn mazes, choosing just the right pumpkin at a local farm, and cheering at kids’ soccer games. Oh – and apples! Lots of apples! Apple picking, apple cider … apples, apples, apples! So, what is it that really says fall to you, where you live?


Our Facebook fans might’ve already seen these photos, but we seriously can’t get enough apples this season! We’ve had such fabulous and delicious trips to our local orchards!

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Healthy Apple Cobbler Muffins

Preparation 20 min. 2017-08-17T00:20:00+00:00 Cook Time 15-18 min. (plus cooling) 2017-08-17T00:00:00+00:00
Serves 18 muffins     adjust servings



  • 1 cup whole wheat flour
  • 1 cup unbleached, all-purpose flour
  • 4 teaspoons cinnamon
  • 1 teaspoon salt
  • 1 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon ground ginger


  • 2 eggs, lightly beaten
  • 3/4 cup packed dark brown sugar
  • 1/2 cup unsweetened applesauce
  • 1/4 cup apple juice (or apple cider)
  • 1 tablespoon canola oil
  • 2 teaspoons vanilla extract


  • 2/3 cup quick oats
  • 1/2 cup chopped walnuts
  • 1/3 cup packed dark brown sugar
  • 1 1/2 - 2 tablespoons unsweetened applesauce
  • 1 tablespoon butter
  • 1 teaspoon cinnamon


  • 1 1/2 cups peeled, shredded Pink Lady apples or other sweet-tart apples (from 1-2 apples)
  • 1 1/2 cups peeled, shredded Granny Smith apples (from 1-2 apples)


  1. Preheat oven to 400°. Line muffin pans with 18 foil liners.
  2. In a large bowl, combine all dry ingredients and stir well with a whisk until evenly combined.
  3. In a medium bowl, combine wet ingredients and whisk thoroughly.
  4. In another medium bowl, mix cobbler toppings, cutting in the applesauce and butter (the easiest way is with your fingers) until evenly distributed.
  5. Mix wet ingredients into the dry ingredients, stirring just to combine and being careful not to overmix. Add the shredded apples to the batter and stir again briefly, just to combine.
  6. Spoon batter into prepared muffin liners, filling each about ¾ full.
  7. Divide the cobbler topping evenly, about 1 heaping tablespoon per muffin.
  8. Bake for 15-18 minutes or until a toothpick comes out clean.
  9. Cool in the pans for about 5 minutes or until the muffins are beginning to set and are cool enough to handle. Remove the muffins to wire racks to cool completely.


Recipe Notes

The wet ingredients, dry ingredients, shredded apples and cobbler topping can all be prepared and kept in separate plastic-wrapped bowls in the fridge (the dry ingredients on the counter) until you are ready to combine everything together and bake. For best results, however, we recommend that you don't mix the apple sauce and butter into the cobbler topping until the last minute.

These freeze beautifully, so you may want to make a double batch! To freeze, wrap individually and store in freezer bags. They will thaw in about 45 minutes or, after removing foil liner, can be gently defrosted at 50% power in the microwave in about 50-60 seconds.

We'd love to see your photos of this recipe! Follow us on Instagram, Facebook, Pinterest and Twitter and tag @TwoHealthyKitchens!



Healthy Apple Cobbler Muffins (With Easy, Make-Ahead Tips!) — 35 Comments

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  4. These muffins look wonderful! We made a bunch of applesauce this fall and i’ve been on the look-out for healthy recipes that have applesauce in them! I’m looking forward to making them… 🙂

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    • Oh Christine – they don’t just look SO good … they TASTE SUPER GOOD!!! And you’re right – the topping is nothing short of amazing! It’s our favorite part! And it’s this topping that sets these little gems of deliciousness apart from other apple muffins! 🙂 ~G&S

  7. These look wonderful! Apple cobbler (heck, pretty much any dessert that revolves around fruit) is one of my favorite things ever–so in muffin form? I could pretty much eat these all day.

    Love your tips too–I’ve always heard wonderful things about combining different types of apples in all desserts, particularly pies. They all contribute something special!

    • Hi, Laura! You’re totally right! Although it’s not strictly necessary, we’ve had great success with using at least two types of apples in our baked goods, and often we’ll use even more varieties when we’re making something like applesauce. It really is all about creating more complex layers of flavor by using the flavor profiles from a variety of different apples. Oh … and about the possibility of eating these all day? Ummmmm … let’s just say that’s worked well in our own test labs (tee-hee)! 😀 ~ Shelley

    • It tastes like a treat – but these muffins are totally guilt-free!!! My kids eat them for breakfast, my husband eats them for dessert! My favorite is the crumble topping … it’s crunchy and delicious and just … YUM!!!! Hope you love these, Pamela!! 🙂 ~Gretchen

  8. I was JUST talking to my husband about how I wanted to make a “healthy” breakfast apple crisp – but this recipe is even better! I mean…a grab-able muffin of apple cobbler? Yes and yes. Love the idea of applesauce in the crumble topping too!

    • Hi Liz!! We love how these taste like the classic delicious fall treat, yet are totally easy to grab on your way out the door! Best part – you can feel so good about munching on one, or two, or …
      My husband actually eats these for dessert, but I love them for a mid-day power-me-through-the-rest-of-the-day snack! 🙂 ~Gretchen

    • Thanks, Mary! You’ve gotta try these! With the sweet apples and crunchy, nutty cobbler topping they are just such a treat, but all the healthy ingredients will keep you feeling energized and full (and pleased with yourself that you did something good for your body!). 😀 ~G&S

    • Yes, Kiersten, we are HUGE fans as well! Our families actually cheer (CHEER!!) when there are fresh muffins made! Freezing is so super convenient, too – especially for those really busy weeks where baking a few dozen just isn’t going happen! We hope you try these! 😀 ~G&S

  9. i make similar muffins on my site but they are NOT healthy hahaha these look soooo good and I am definitely going to be making them soon (I still have to make your chocolate pb ball bites). I really love your tips for making the recipe easy too. thats probably the worse part of cooking ,the prep and the mess. when i make the recipe, i will prep the nigh tbefore so i can easily bake them off the next day! thanks 🙂 have a great weekend!

    • Hey, Christina! I’m so happy you’ve got a running list of THK recipes you’re excited to try – that’s quite a compliment! And, yes – I totally feel your pain on the prep/mess issue – I feel like I am CONSTANTLY cleaning up the kitchen AGAIN! Worst part of being a food blogger, right – the endlessly messy kitchen!?!? I need to get some kitchen clean-up minions! Like, real minions who aren’t in school all day! (Unlike my taste-testing minions who swoop in from the bus and gobble up all my hard work before they dash off to do homework … leaving me in the middle of my still-messy kitchen!). 😀 ~Shelley

    • Perfect timing! I actually have a kitchen FULL of apples since Gretchen and I have been cooking up a veritable storm of apple recipes. They’re in bowls and bags all over my counter and stuffed throughout my fridge! I guess you and I both need to get baking! 😀 ~Shelley

  10. These look too great to be true: healthy, freezable and delicious-looking (and tasting, I’m sure!)… I need to make them as soon as possible! It’s such a pity that we don’t get Pink Lady apples here… it’s definitely my favorite apple and I haven’t eaten one since I last travelled to Ireland :(( Do you think that Royal Gala would work here? x

    • Hi, Consuelo! That is such a bummer that you can’t get Pink Ladies, but not to worry! Any good baking apple will do – the flavor may vary a bit (Pink Ladies are sort of sweet-tart, of course), but that’s ok, right!?!? You may be able to find Pink Ladies sold under the varietal name Cripps Pink. Honestly, that’s often what I find at my local market and use just as I would use Pink Ladies. If I can get all geeky on you for a minute, I think this is super-interesting: according to, in order to be sold under the trademarked name Pink Lady™ the Cripps Pink apple has to meet strict requirements, and actually over half of the Cripps Pink crop typically doesn’t. (Those, then, are sold under the name Cripps Pink instead of being able to be labeled as Pink Ladies). Huh! Also, I think your idea of Gala might be very nice here, although it will probably yield a bit more sweetness that the Pink Lady. You might also try other sweet-tart apples with a firm flesh, such as Honeycrisps, or maybe try Braeburns or Cortlands. I hope that helps. Seriously, though – just grab some apples and bake these up quick – they are soooooo good! 😀 ~Shelley

  11. Yum, these looks applelicious!! 🙂 Great minds think alike…I just made some apple muffins 🙂 Aren’t they just perfect for fall. I’ve been mixing apple into everything! I’ve gone a bit apple-crazy. Lol I love that you added walnuts into your crumb topping, I’m going to try that next time 🙂

    • Hey, Cindy! Yup – we’re apple crazy, too! And, definitely add those walnuts! It’s really the crunchy cobbler-like texture of the topping on these muffins that makes them so unique (and beyond-delish!). 😀 ~G&S

  12. YUM!!!! I just made some apple muffins this morning that is very similar to this recipe. I used all soft white whole wheat that I ground myself. My recipe called for buttermilk and applesauce. I used sucanat in place of the brown sugar.

    I need to try this recipe too.

    • Ok, so how totally impressive is it that you grind your own flour!?!?! So fantastic! 😀 Buttermilk is a wonderful liquid for low-fat baking, and we use that a lot, too. You could definitely give it a try here, although we liked the apple juice to further amp up the apple flavor. (Plus, would you be surprised to learn that we tend to have a lot of kids’ apple juice boxes in the fridge!?!?). Regardless – give this recipe a try! ~G&S

    • Hi, Lori! Yeah – fall really is pretty awesome (for lots of reasons, but maybe most especially for all the cozy-yummy foods that come along with it)! So glad you thought the make-ahead tips were helpful – we will definitely keep the easy-to-make recipes and quick tips coming your way! ~G&S

    • Hi Melanie! These muffins will be perfect for you! They are totally delicious, but wonderfully healthy! Our families have been having these for dessert (many test batches!) and were totally happy and satisfied! Let us know if you love ’em! 🙂 ~G&S

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