Healthy Sourdough Pumpkin Apple Muffins With Ginger & Streusel

These sourdough pumpkin apple muffins are delightful for breakfast, coffee break treats or on-the-go snacks. Wholesome, healthy, delicious! 

Try these delicious breakfast muffins that will satisfy your sweet cravings and your appetite with wholesome goodness that works for your health, not against it. And healthy can be delicious and flavorful! If you like to make each bite count for nourishment but like to have a bit of sweet and something that feels like a treat, these are for you. 

And they are easy to take along if you’re a busy family. Make these ahead and long-ferment them for up to 4 days for increased health benefits. And you can bake and freeze them for your busiest days and know that you’re prepared when your loved ones come in hungry from a hard day of play or work and you’ll want something wholesome and healthy for them.

Let’s get to it!

Try also my Pumpkin Cake with Apple & Ginger Streusel for a tasty holiday breakfast or to serve your guests. And if you are a fan of apples and healthy treats, you’ll love my Apple Pie Cheesecake Bars and the fabulous Ginger Spice Apple Crisp With Cranberries! For guilt-free dessert indulgence give my Lemon Cheesecake Mousse a try. And for more fruity and healthy recipes, check out my amazing Blueberry Cheesecake Bars and Blackberry Cobbler, a purely cozy comfort food. For more healthy autumn treats I recommend Sweet Potato Bread and Spicy Lemon Tahini Cookies. 

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Sourdough Pumpkin Apple Gingerbread Muffins

I wanted to share this little fall recipe before I get into more Christmas baking, because it is a wonderful treat for fall and winter. It’s full of warm spices that will fill your home with a comforting scent that makes staying indoors so cozy when the cold winds blow outside.

And you’ll get a healthy dose of antioxidants and anti-inflammatory compounds to help steel your immune system for the cold season. In addition you’ll get better digestability and absorbance of the nutrients when you long ferment them.

I think this recipe will conclude my recent apple baking streak because I’m finally reaching the bottom of the bucket of picked apples for this year. It’s a bittersweet thing, but there are many other delicious things to bake and cook up, and then there are cheeses and herbal salves, and other good things that I’ve been wanting to write about. So let’s make another delicious recipe with apples before I run out here and then we’ll resume this series next fall!

And if you love healthy fall treats, try my delicious cranberry ginger applecrisp and pumpkin apple cake too!

Why You’ll Love This Recipe

• These muffins are wholesome, healthy and delicious. They are brimming with ingredients that are supportive of your health with just a bit of sweetness added to make your ‘medicine’ taste awesome. I like to load up on antioxidants for the winter and support my body with anti-inflammatory ingredients, and that was the inspiration for this muffin recipe. You won’t get a super sweet coffee cake taste, instead these muffins are hearty, wholesome, and healthy enough to start your day with.

• We’ll be using fresh-milled ancient grains to make the flour for this recipe. Such a healthy alternative to white flour, which has all the best parts removed. You still can use white flour in place of the whole grains though, so if that is what you prefer, I won’t try to sway you! Ancient whole grains are easier to digest than modern wheat and are often tolerable for people with wheat sensitivities. And they add vitamins, minerals and healthy fats along with a delicious nutty flavor when freshly milled.

• Unrefined sweeteners: I like to cut refined sugar out of my diet as much as possible, safe for a bit of chocolate here and there, but I do like some gently sweetened baked goods now and then. So in this recipe we’ll use a couple of my favorites, panela sugar (sucanat) and maple syrup. They are made with unrefined, concentrated sap from cane sugar and maple trees. These have important minerals and nutrients in them and substances that work in synergy together, to help our body use these nutrients and digest the sugars much more easily. If you like them sweeter, just increase the sugar a bit or add more topping and they’ll turn into dessert muffins. They’ll be light and fluffy either way.

• Long fermentation: You can also long-ferment the dough to lessen the sugars and increase the tang in your muffins just a bit. But more importantly, you’ll increase the health benefits, an important consideration for starting your day off right. My favorite muffins are long fermented for about 48 hours for a great flavor, but you can let them ferment for 3-4 days. Long fermentation will make them easier to digest, break down phytic acid and increase nutrient availability. Plus I find they taste best after about 48 hours of fermenting.

• Apples and pumpkins are dense with vitamins and minerals that are beneficial for our heart health, eye sight, and can even fight some cancers. (source, source)

• Immune Support: Finally we’ll load these up with spices that help reduce inflammation, fight free radicals, support immune functions, and support heart, gut, and brain health! Learn more about the health benefits of turmeric in my posts fermented turmeric and how to make turmeric tincture. And learn about ginger in my articles Health Benefits Of Ginger Beer and Fermented Ginger Honey

• Love it yet? You will really love them when you taste them! They are delicious and make it easy to want to eat clean, real food. Let food be your medicine!

Disclaimer: The material and nutritional notes on this site are intended to be for general informational use and are not intended to constitute medical advice, medical diagnosis, or medical treatment. You should consult your physician or other health care professional before making any changes in your diet. All health claims are not to be used as facts and I am not responsible for misuse of this information. 

Tips and Substitutions For The Best Sourdough Pumpkin Apple Muffins

• I’ve made these several different ways, and this way is my favorite, but you can adapt to what you prefer or might have on hand. After grinding my own flour for years, it would be hard for me to go back to pre-ground flour. The flavor of fresh milled is just unbeatable. But these muffins can be made with purchased bagged whole grain flour or all purpose flour. I recommend you weigh the flour, since there can be a huge difference between fresh milled and bagged flour, and also between whole grain and all-purpose. 

• I find these muffins plenty sweet, but I want to point out that these are less than half the sugar of comparable recipes and if you’re a big sweet tooth, you might want to add just an extra 2 tablespoons of panela sugar or maple syrup. Or double the streusel topping and layer your batter with some extra streusel when you assemble the muffins. 

• Use pecans instead of walnuts for the streusel, or try other nuts or seeds. Use sprouted or soaked nuts and seeds for better nutrient availability. Just soak in some salt water or whey for 24 hours, dry and use as usual.

• Use chopped crystallized ginger instead of fresh ginger. This will make your muffins sweeter and the ginger will taste more like candy and less spicy. I love using the crystallized ginger, it is super delicious, but I also like the less sweet and more pungent taste of freshly chopped ginger, especially in this recipe where I try to keep the sugar down. 

• Use raisins, chopped dates, or dried cranberries instead of or together with the ginger. 

• I recommend using the deeper tulip muffin liners for these muffins to make them a bit larger and to keep the topping contained. I didn’t have any, but they are easy to make. Just follow the instructions below!

How To Make Your Own Tulip Style Muffin Liners

For 12 muffin cups just cut a 20″ piece of 15″ wide parchment.

Fold the long side in half and again in half. Then fold the long way into thirds.

Open it and use scissors to cut along the lines and you’ll end up with 12 pieces that are 5″ square.

Now take a glass that fits into the muffin cups. I used a small juice bottle but an 8 oz jelly jar will work too.

Turn the jar upside down and center one of the squares over it and press down the sides. And you’ll have a beautiful muffin pan liner. Repeat for all the squares.

The benefits of these are four-fold.

• They can hold a little more muffin batter and you’ll get bigger muffins and less spilled topping.
• And the muffins don’t stick to the paper like they do with the little purchased fluted ones.
• You’ll get wonderful little ‘handles’ to easily remove your muffins from the tray without dumping and spilling a bunch of the streusel.
• They save money over already made liners.

They don’t take long at all to make, you’ll have 12 liners done in about 5 minutes.  

If you’re anything like me, you’ll reuse them a few times. Just wipe off the crumbs, and fill again.

If you want to make them a little bigger, just use 6″ squares, but it won’t make such efficient use of the parchment, which normally is 15″ wide.

How to make Sourdough Pumpkin Apple Ginger Muffins

Here you’ll find my notes and recommendations on equipment, tools and a visual step-by-step guide to making these muffins. For exact measurements check the recipe-card.

Tools You May Need

Grain mill – You’ll need a grain mill if you want to make fresh milled flour. If you don’t own one yet, I highly recommend the Mockmill. It can grind superfine to coarse flour and the flour does not get overheated in the process. It takes up little room on your counter and gets the job done quickly. Plus it’s made to last! In a pinch you could use your blender.

A few bowls – You’ll need a large bowl for mixing the batter and a small one for mixing your streusel. You can melt the butter in a measuring cup or another small bowl. I usually use another small bowl for mixing the flour and sifted leavening (baking powder and soda).

Assorted measuring cups and spoons

Apple peeler – You can peel your apples or leave the skin on. I peel mine when the skin looks less than perfect from storage, but if it looks good I don’t peel them. I love this Linden peeler. For bigger apples and when I have a large amount to peel, I like to use my apple peeler slicer corer. If you purchase apples that are not organic, you’ll want to peel them.

Paring knife – for cutting out bad spots and coring your apples. I like to use my small Victorinox paring knife.

Kitchen knife + Cutting Board – for chopping the apples and ginger.

Hand mixer – For mixing the batter or you can use a wire whisk or egg-beater.

Scale – optional but highly recommended. I use a scale to make adding ingredients easier and have less dirty measuring cups. But it also helps to be consistent, since the different flours and sweeteners vary much in weight when using the same volume measure.

Parchment paper or muffin liners – use this for lining the muffin cups. If you’re using aluminum or coated muffin pans, I highly recommend lining them to avoid exposure to any toxins in the coating or the material. But you can also just butter and flour the pan. If you don’t have liners, you can make your own easily, see instructions above. Lining it makes it easier to take the muffins out later and these homemade ones can hold a little extra batter for bigger muffins. Making your own is really easy, quick, and saves money.

Muffin pan (18-24 cups) – This recipe will make 18 large or 24 regular sized muffins.

Cooling rack – Take your muffins out of the pans so they don’t get soggy after baking and let them cool on a rack.

Ingredients

I choose organic ingredients for my cooking and baking for health reasons. Organic ensures that my ingredients aren’t irradiated, full of pesticides, chemicals, and other toxic additives that can likely cause inflammation and other health problems. And it ensures that I can avoid any GMO ingredients. A non-GMO label is sadly not enough. Even most non-GMO foods are heavily doused with toxic pesticides if they are not organic.

Growing your own food is the best way to assure clean food, and you’ll know what you are putting on it. And if that’s not possible, choosing organic whole foods, and especially produce from regenerative farming operations, will go a long way towards a better chance to keep healthy and thriving. Conventionally grown apples have been tested high for pesticides and chemicals and are on the EWG’s dirty dozen list for 2025!

For The Muffins

Butter – I like to use Kerrygold from pastured dairy cows. Unsalted or salted butter is fine, but if using salted butter, cut down on added salt. Butter gives a rich flavor to your muffins.

Avocado oil – Oil helps to keep the muffins moist. You can use all butter or all oil. But I like to use equal amounts of both.

Eggs – I raise my own chickens for eggs, but if I didn’t I’d try hard to find eggs from organic, farm fresh, pastured chickens.

Panela sugar – I love panela sugar for a nice gingerbread flavor. It’s the unrefined sap of sugar cane, reduced by boiling it down and drying it until it is crystallized. It contains the nutrients and molasses that are normally stripped away from refined sugar. Other names for this sugar are jaggery or sucanat. A good substitute would be coconut sugar. If you prefer to use white sugar, I recommend pure cane sugar, since most commercial white sugar and brown sugar is made from GMO sugar beets.

Maple syrup – Another unrefined concentrated sweetener that I love with baked pumpkin recipes. Mild flavored honey is a great substitute.

Pumpkin puree – If you’re using homemade, be sure to drain it well. Hang it in a cheese cloth or use paper towels to pat it to get some moisture out.

Sour cream or quark cheese, clabber, buttermilk or yogurt – I used quark cheese, but any of these will work for moisture and a nice tangy flavor.

Sourdough discard or active sourdough – if you don’t have sourdough, check out my article for making your own sourdough from scratch. But if you want to make this recipe right now, you can just leave it out. It will still work because the sour cream, quark, or yogurt will be sufficient for an acid ingredient and for moisture. And if you choose a probiotic live dairy product you can still opt to long-ferment with your dairy-based lacto-bacilli even without sourdough and you will achieve similar health benefits and the breaking-down of the phytic acid.

Vanilla extract – I prefer to use organic vanilla. You can get it in bulk from Azure Standard for a good price, or make your own, here is a great recipe. You could also use scraped vanilla bean seeds if you have them.

Fresh milled ancient grain flour – In this recipe I prefer fresh milled flour made with a mix of half Kamut® (Khorasan) and half einkorn berries. The Kamut flour gives the batter a bit more strength and absorbs some of the moisture better. The einkorn flour is unmatched in flavor in my opinion and I love to bake anything with it. They are both considered to be ancient grains and are generally much easier to digest and utilize by our bodies than modern grains. Many people with wheat intolerances report having no issues with einkorn, Kamut, and other ancient grains. If you are not into grinding your own, you can purchase einkorn flour and Kamut flour pre-ground. All-purpose flour works too, but will alter the texture and flavor.

Baking powder – This adds leavening. The sourdough will not contribute to the rise on same-day muffins, since this is a quick bread, so we need the baking powder for this. Here is a recipe to make your own baking powder.

Baking soda – This is another leavening agent that will work together with baking powder to achieve a good rise for a fluffier cake.

Sea salt – I like to use Redmond’s Real Salt or Himalayan pink salt to add essential trace minerals to my diet.

Apples – Chop the Apples, peeled or unpeeled, your preference, although I recommend peeling if your apples are conventionally grown and have been sprayed. If you don’t grow your own, I recommend Granny Smith or Honeycrisp apples for baking!

Ginger – I used finely chopped fresh ginger, which is my preference when I can get it. Or you can use grated ginger if you don’t like the pungent chewy bits (I love them!). If you have fermented ginger paste, you can just stir 2 tablespoons of that into the batter instead which is a little milder.

Optional: use crystallized ginger pieces instead of the fresh. I love ginger and crystallized ginger is a bit of a weakness of mine. And they are so delicious in baking! The ones I’m linking to are organic and are sweetened with cane sugar. If you make your own, use that! If you’re baking for kids and you want a less spicy taste without omitting ginger, these crystallized bits are great to use. If your kids like to eat the crystallized ginger, then they will likely not object to having them in the muffins, but use your own judgement on that. You can also just use a bit of ground ginger powder instead.

Other spices (You can substitute 1 Tbsp pumpkin pie spice instead)

Cinnamon, Nutmeg, Cardamom, Allspice, Cloves, Ginger – These will give that traditional pumpkin spice flavor that we all have come to associate with fall and holiday baking plus I like to add a few of my own preference. Cardamom is not so common in America, but it’s well-loved in European baking and I prefer using it for its great flavor and its powerful health benefits. The ginger can be in addition to the ginger bits for an overall gingery flavor. You can omit it if you want less ginger or use it as your only ginger if you’re not using chopped fresh ginger.

Turmeric & white pepper – I like to add turmeric to many of my spiced recipes for its powerful health benefits. It lends little flavor, but a big healthy punch and a lot of color to your baked goods. I always pair it with pepper for better absorbancy and white pepper is also used in German holiday baking and works great with spiced sweets. Pepper tends to increase absorbance of all the potent nutrients that live in all the spices we use here, and so your health benefits are increased just by adding a little pepper. Pepper should be fresh ground for this benefit. I am linking to whole peppercorn here.

For the Streusel

Walnuts or pecans, chopped or crushed – I use my mini sledge hammer for crushing mine, so I have a nice mix of fine to coarse. If you can, soak your nuts or seeds for improved health benefits. This will break down phytic acid and increase nutrient availablity and absorbancy.

Fresh milled flour, any kind – I used the same mix as for the batter, but most of the time I use just einkorn in my streusel. You’ll get a bit of a crunch if you don’t grind it too fine, which I really enjoy.

Butter – salted or unsalted is ok. If you don’t use salted, you can add a pinch of salt to the streusel.

Cinnamon – My preference is ceylon cinnamon.

Panela sugar (sucanat) – Or coconut sugar

Salt

Instructions For Making Sourdough Pumpkin Apple Ginger Muffins

Preheat the oven to 400 degrees.

Line your muffin cups with parchment sleeves or fluted muffin cup liners.

Prepare The Streusel

Melt the butter on low heat, then remove from the heat to cool down a bit. 

Meanwhile, mix the dry streusel ingredients, flour, panela sugar, salt, and cinnamon in a small bowl.

Add the chopped walnuts.

Pour the butter over your dry streusel ingredients and mix with a fork or spoon till evenly moistened. Set aside.

Mix The Muffin Batter

Chop your apples and ginger before you start and set aside.

Mix the flours, baking powder, and baking soda in a small bowl and set aside. I always sift my leavenings to eliminate clumps. I hate it when I eat a perfectly tasty muffin and suddenly bite on a clump of baking soda. That ruins it for me, lol.

Place the softened butter and avocado oil in a bowl. 

Add the panela sugar and beat until creamy. 

Incorporate the eggs one at a time, beating after each addition till smooth. 

Dump in all your other wet ingredients maple syrup, pumpkin, sourdough, sour cream, and vanilla extract, as well as the spices and the salt. 

Use your mixer to mix everything till creamy and well blended. 

Mix in the chopped ginger.

Dump your flour mix and chopped apples over the wet ingredients. Then use a spatula or spoon to  incorporate gently and until just mixed. Resist the urge to over-mix. A few streaks of flour showing is ok. 

At this point you can put the dough into a sealed container, and leave it at room temperature for a couple of hours, then place the dough into the fridge for up to 4 days to long-ferment. Then proceed.

Assembly

Use a spoon or scoop to fill your muffin cup bottoms with half of the batter.

Add a layer of the streusel, using half of the streusel mix.

Fill all the cups the rest of the way with the remaining batter and top with the rest of the streusel. With homemade liners or purchased tulip liners you can fill the cups to the top.

With purchased fluted liners, keep it just under the edge of the rim. You’ll get more muffins that way but they’ll be smaller, and a perfect size for kid parties.

Bake for about 20 minutes or until a toothpick stuck into a center muffin comes out clean (or with just a few crumbs attached).

Let cool for a couple of minutes, then remove from the muffin pan. Invert the whole pan onto a baking sheet, then flip them back over onto a cooling rack. Or use your homemade liner points as handles to pull them out. Cool them on a cooling rack inside the sleeves.

Enjoy!

Storage

These are best fresh. They will keep for a day at room temperature. Refrigerate them after a day or the moist apples will start to ferment. They’ll keep for 3-4 days in the fridge. For longer storage, freeze them. Wrap them singly for best results. First tightly with plastic wrap or parchment, then aluminum foil, or put the wrapped singles into a freezer bag, or a freezer container.

When you want to enjoy one, take it out and defrost at room temperature. Or put it in a 350 degree oven and heat until toasted on the outside and warm on the inside for that great fresh-baked flavor and texture. 

Your Questions Answered

Enjoy Sourdough Pumpkin Apple Ginger Muffins

These muffins are so delicious, full of fall flavors and cozy fall aroma. Your kitchen will smell so wonderful, and invite feelings of comfort. These are great for breakfast whether on the go, or at home, and they are so delicious for coffee break or teatime. If you’re an outdoorsy type, they pack well for pick-me-ups and a bit of energy on the trail or road trips.

You can add extra streusel as a middle layer for more sweetness. Or leave them out completely if you’re trying to cut down on sugar. However, I think it rounds these muffins up perfectly without being too sweet. So I hope you’ll give these a try and I’m sure you’ll enjoy them as much as I do! 

Have you made these pumpkin apple ginger muffins? I’d love to get your feedback and your ⭐⭐⭐⭐⭐ rating if you like this recipe! And I’d love to hear your favorite ways to use Sourdough Pumpkin Apple Ginger Muffins. And please don’t hesitate to ask in the comments if you have any questions!

Join the Food For Life Garden Community for more great recipes and homestead tips and ideas. I’m always adding new content. Don’t miss any new posts and learn more about my off-grid farm life.

Other Recipes You Might Like

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Ginger Spice & Cranberry Healthy Apple Crisp – This most delicious, comfy and cozy fall and holiday dessert will warm you up on a chilly day and fill your home with the delightful scents of apples and spice and everything nice.

Sweet Potato Bread Recipe – A delicious spiced sweet bread that’s great for breakfast, tea time, a snack or as a side at dinner. It’s scrumptious slathered with real butter!

Sourdough Discard Blackberry Cobbler – A must for summer and blackberry season. Don’t have your vanilla ice cream without it. Super delicious and healthier than traditional versions too!

Soft Sweet Potato And Peanut Butter Cookies are a delicious snack for anytime. Loaded with healthy ingredients that give these cookies a distinct and delicious flavor. Great for lunch boxes, trail food, tea time, snacks and more.

Einkorn Zucchini Bread – Make this delicious zucchini bread that is moist, healthy, and doesn’t skimp on flavor! Delicious!

Lemon Blueberry Cheesecake Bars – Creamy, with a buttery crust, this cheesecake dessert is bright, tangy, easy, and perfect for summer gatherings, or any sweet cravings!

Best Flaky Pie Crust – Check out my best flaky pie crust recipe. Perfect for all your harvest and holiday pies! Lost of options for customizing.

Probiotic Ginger Paste – A convenient way to have ginger on hand when you need some, either as seasoning in cooking or baking, or to use this powerful ally in your daily health routine.

Lemon Cheesecake Mousse – A decadent, delicious, super healthy lemon dessert made with honey & lemon curd.

Lemon Tahini Cookies – Delicious, healthy spice cookies with lemon and honey. These spicy cookies are radical, especially if you love bold, complex flavors and healthy treats.

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Grain mill
Muffin pan
Paring knife
Linden peeler
Peeler slicer corer
Parchment Paper
Muffin liners
Knife
Cutting Board
Panela sugar
Evaporated cane juice
Coconut sugar
Maple syrup
Honey
Redmond’s real salt
Himalayan pink salt
Kamut® berries
Kamut® flour
Einkorn berries
Einkorn flour
Ceylon cinnamon
Nutmeg
Cardamom
Allspice
Cloves
Ginger
Turmeric
White pepper
Walnuts
Crystallized ginger pieces
Organic vanilla. You can get it in bulk from Azure Standard