We’ve been making these muffins for years!
Not only are they super easy and flexible, they’re really scrumptious.
Make these whole grain muffins as-is, or use the general formula of this recipe to use your own add-ins and flavors. Enjoy!
Why Soaked Muffins?
Whole grain flours, just like whole grains, contain phytic acid and enzyme inhibitors. The grain was ground up into flour, but nothing’s been done to neutralize these anti-nutrients that would inhibit mineral absorption or prevent optimum digestion.
When we add a soaking stage to a recipe, the soaking of the flour in an acidic liquid neutralizes some or most of the phytic acid. And, the baking deactivates the enzyme inhibitors.
Soaking is very simple. You combine the flours/grains in a recipe with liquid (water or milk) and an acid.
Then you let it “soak” for 7 to 8 hours or overnight. Finally, you bake!
You might also be interested in the Basic Sprouted Muffin, which uses sprouted flour. Sprouted flour digests like a vegetable, and sprouting also neutralizes phytic acid and increases certain vitamin levels.
Whole Grain Soaked Muffins
A family favorite, these whole grain soaked muffins are super easy and flexible! Gluten-free? Check! Dairy-free? Check! It's a simple recipe formula that consistently delivers gut-friendly, delicious muffins perfect for breakfast, snacks, or even dessert! With one basic recipe (and FREE video instructions!), you can make lemon poppyseed, chocolate chip, cinnamon apple... any flavor you love or crave. Kids love them, and so do adults.
- 1-1/2 cups whole wheat pastry flour or whole wheat flour, spelt flour, or einkorn flour (or your favorite gluten-free flour blend or homemade gluten-free blend by mixing equal parts buckwheat, millet, sorghum and sweet rice flours)
- 1/2 cup rolled oats
- 2 tablespoons raw apple cider vinegar or whey, lemon juice, Kombucha, water kefir, yogurt, dairy kefir, or sourdough starter
- 1 cup raw milk or best you can buy (or non-dairy milk of choice)
- 2 organic or pastured eggs
- 1/2 cup Rapadura or Sucanat, or evaporated cane juice
- 1 teaspoon vanilla extract
- 1/2 cup coconut oil melted
- 1 teaspoon sea salt
- 2 teaspoons baking powder
- 2 teaspoons ground cinnamon optional
- 1 teaspoon ground ginger optional
- 1/4 teaspoon ground nutmeg optional
- 1/2 cup raisins optional
- 1/2 cup soaked and dehydrated nuts optional
- 1/2 cup unsweetened shredded coconut optional
- 1 cup shredded apple or zucchini or carrot (additional moisture may require additional cooking time)
In mixing bowl, combine flour, rolled oats, apple cider vinegar, and milk.
Cover and let soak overnight, up to 24 hours.
When ready to bake, preheat the oven to 375 degrees Fahrenheit.
In separate mixing bowl, whisk together eggs, sweetener, and vanilla.
While whisking (to avoid cooking the eggs if the coconut oil is on the warm side), add in the coconut oil.
Whisk until smooth.
Add salt, baking powder, and spices to the wet ingredients. Whisk fully.
Add wet ingredients to the soaked flour mixture. Mix until smooth. It may take 3 to 5 minutes because the flour mixture gets thick and pasty during the soaking time.
Add add-ins and mix to incorporate.
Fill oiled muffin tin (or paper- or silicone-lined muffin tin) with the batter to a generous three-quarters full each.
Bake for 20 to 25 minutes, until a toothpick inserted in the center of a muffin comes out clean and muffins are golden brown.
Take out of oven and transfer muffins to a cooling rack.
If using paper or silicone liners, allow to cool for 15 minutes before trying to pop one of the liner. Store in an airtight container when fully cooled. Keeps a few days.
Refrigerate to keep good up to a week. These freeze beautifully!
**Egg substitute. Mix together 2 tablespoons ground up flax seeds or chia seeds with 6 tablespoons water. Allow to sit for 5 minutes to gel. Whisk with the sugar, then proceed with the rest of the recipe.
Looking for other healthy muffin recipes? Check these out!
- Healthy Gluten-Free Double Chocolate Zucchini Muffins (Paleo)
- Soaked Apple Cinnamon Muffins
- Chocolate Chip Banana Muffins (Gluten-Free)
- Blueberry-Lemon Muffins
- Coconut Sourdough Muffins
Do you have a favorite muffin recipe? Will you try these soaked muffins?
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I have the Nourishing Traditions book. I’ll have to look up why you want to soak and they dehydrate the nuts. Do you have to have nuts in the muffin? I have everything, but the coconut oil.
.-= Michelle´s last blog post… Awesome Cells! =-.
Michelle – the nuts are just optional – you add whatever add-ins you want. Nuts, raw (as-is), contain enzyme inhibitors – the process of soaking neutralizes those inhibitors (when germination begins). Then dehydrating the nuts gets them back to that crispy stage you need for chopping, snacking, etc. If you soak them in salt water they taste really good, too!
Michelle – also, you can use butter for the oil.
.-= Michelle´s last blog post… Awesome Cells! =-.
Looks like a fantastic recipe! I’ve actually been looking for an easy soaked muffin recipe with low sugar and coconut oil. Thanks.
.-= Maria´s last blog post… Beach Vacation =-.
Maria – The amount of sugar is flexible – Millie only uses 2 tablespoons. With 1/2 cup, these are still sweet. The sweetener could be lowered to 1/4 or 1/3 cup easily.
Sonya Hemmings says
Wardee, these muffins look really good and sound delicious! Where do you get your whole wheat pastry flour?
.-= Sonya Hemmings´s last blog post… On My Plate: Birthday Cakes =-.
Sonya – In the past, I have purchased from health food stores’ bulk bins. But usually (like this time) I grind my own *soft* wheat berries.
Yum! I’ve made soaked muffins before but these look better than anything I’ve tried.
.-= Leah´s last blog post… read this! =-.
Leah – hope you enjoy! I’m licking my lips right now – just ate one! 🙂
This looks great… I might just have to try it out soon myself! Thanks 🙂
.-= Alyss´s last blog post… Nothing Says Lovin’ Like Something From the Crockpot =-.
Tried these today and they were delicious! This recipe is a keeper. Thanks for sharing.
If all I have is hard white wheat berries what should I change about this recipe? That is the only kind of wheat I buy and I buy it in huge quantities, so I like to stick with it for all my baking if possible.
Kim, you wouldn’t change much. Perhaps you would use 1/8 cup less flour (2 T). Or you can add a bit more milk at the end if the batter is too thick. Other than that… the same! Please let me know how it goes!
I’m looking forward to trying this recipe as I’m still seeking for the perfect soaked muffin! What do you think about using kefir or yogurt rather than the milk/vinegar – is that something you already experimented with?
Susanna – I think that would work. I just started a batch like that this morning and can tell you later how it goes. I used 1 cup of kefir and omitted the apple cider vinegar. It might be too thick depending on the thickness of the kefir, but it is easy to add more liquid when mixing up the batter.
Great – definitely let me know how they turn out as compared to when you use the milk/vinegar. Thanks!!
Susanna – The consistency was perfect. In fact, no difference at all. The only difference was that because the kefir is sour and the raw milk is not, these muffins ended up needing a bit more sweet. When I do this again, I’ll add 2/3 cup of sweetener, perhaps a scant 2/3 cup. Enjoy!
I’m allergic to cow dairy – can I still make these muffins? I was planning on using store-bought hemp milk…do you know if this is okay to leave out at room temp? Should I just make my own raw nut/seed milk and use that? Or can I just use water? Or yogurt (I buy the goat version)? And to make a long story short, I don’t do goat milk. What are my options?
Vanessa – Use any milk or water – it’ll all be fine sitting out at room temp. Make sure to use the acid (apple cider vinegar or Kombucha). Enjoy!
Hi there- are the oats soaked at all?
Hi, Jessica – Yes, the oats are soaked along with the whole wheat pastry flour.
Could I use lemon juice for the acid?? My ACV didn’t come in our co-op shipment this month. 🙁
.-= Anjanette´s last blog post… Split Pea and Sausage Dahl =-.
Anjanette – Definitely! You could also use whey, yogurt, kefir, or buttermilk, as long as they have active cultures.
I just wanted to leave a follow-up comment that this recipe was fantastic! I soaked with a combo of kefir/yogurt and added a bit of water (to replace the vinegar liquid). Also, I upped the sucanat slightly as you suggested. They were so delicious and were great the first and second day. The ones I froze (immediately) were a bit crumbly when we used them, so I won’t be making tons to freeze, but will definitely use this recipe again! Also, doubling it and using the Bosch to mix is much easier than stirring by hand. My kids watched your muffin tutorial yesterday and loved it. 🙂
Susanna – Cool! I’m glad you liked it.
Nancy O'Larnic says
I made the muffins tonight and they are delicious. However, I have a few questions.
I purchased coconut oil in solid form. I measured 1/2 a cup of solid coconut oil in a dry measuring cup and melted the oil as the recipe instructs before adding it to the egg/sugar mixture. When I measured the melted oil it was over 1/2 a cup (between 1/2 and 2/3). I placed all of the melted coconut oil to the egg/sugar mixture. Is that correct?
I am attempting to eat more nutrient dense foods (such as these muffins). However, I am working on reducing my weight by 30 pounds so my calorie intake is also important. How many calories are in one muffin with no add-ins?
Thanks for your help.
Nancy – I measure mine in solid form and then melt it. So you did it just right – I never measure it when it is melted. However, it is flexible – so you would have been fine regardless.
As to the calories, I do not know. I never count calories. You could probably find an online calculator – input the ingredients and divide the total calorie count by 12 (if you yielded 12 muffins?).
I’m glad you enjoyed them!
These were wonderful! My whole family loved them. Thanks!
Nancy – I put all of the ingredients into my calorie counter software (I too am looking to shed a few pounds!) and making 12 muffins, they came out to:
206 calories each
11g fat (8g saturated)
25g carbs (3g fiber)
I’ve got my flour soaking now…. can’t wait to bake the muffins (and eat them!)
.-= Shelly @ EpicOrganic.net´s last blog post… Getting Ready for Muffin Goodness =-.
Amanda Kaake says
I’m making my first batch of muffins and am so excited about it. My question is, can I use raw honey or a combination of honey and maple syrup for the sweetener? How about stevia?
Thank you so much for all you do!
Amanda Kaake says
I did a combination of maple syrup and honey to equal 1/2 cup. I cut down the coconut oil just a bit and baked them at 350 degrees for 20 minutes. They were so moist and wonderful! I’ve never had that happen with a whole grain muffin. Must be the soaking. I’m very pleased. I’m purchasing rapadura with my hubby’s next check. Oh and I just used water (since we aren’t yet able to get raw milk) and acv. Thanks!
These are amazing! Thank you so much!
We just tried making these today, using filmjölk for soaking liquid and butter in place of coconut oil. Soooo delicious according to my husband and two little boys. Thank you so much for a soaked flour recipe that works:). I faintly remember some failed adventures using NT recipes years ago which has deterred me from using soaked flour in baking. Been using mostly sprouted flour but I haven’t had a decently priced source for the past year, having moved abroad.
I tried these today and was a bit disappointed by the slight taste of ACV in the muffins. I used water instead of milk, so I’m wondering if this caused the ACV taste. I will try these again and next time will use whey for soaking instead of ACV. I had this same thing to happen when I soaked oats in lemon juice for oatmeal.. Disappointing but I’m learning and am thankful for finding this soaked muffin recipe.
EXACTLY!!!! THEY WERE SUCH A DISAPPOINTMENT =( =( ACV FLAVOR THROUGHOUT–TOTALLY BLEGH, GROSS!!!!
Can you make these with gluten free flours ?
Bev — Yes, you can. Download these recipe notes. The PDF has substitutions listed.
Wardee, Thank you so much for this recipe. I just made the muffins and my family loves them! I made your granola yesterday and it’s a hit as well! I am new to traditional cooking. It’s overwhelming at times, but your site and eCourses have been such a blessing to me. We switched from vegan and started following WAPF. I have Rheumatoid Arthritis and since we changed our eating, I have been able to stop dangerous drugs and live a healthier and more active live.
Thank you for all the work you put into GNOWFGLINS.
God bless you,
Sharon from NH
First time to this site and I love it!
When soaking like oatmeal alone are you supposed to drain any unused soaking juice? And would you then rinse the oatmeal? Same for the dry soaked muffin ingredients, do you rinse it after the soaking. LIke with soaked beans, you rinse them before soaking, right?
How did soaking come about. I only see it in the Bible one time, in Ezekiel.
Oh my these are good!! I ended up making them for the first time the other day. I had this guava jam that I attempted to make but it ended up like a solid block of fruit leather (maybe too much pectin?) so I pried it out of the jar, cut it up into pieces, and added it to these muffins. It was delicious! Oh and I left out the spices because I didn’t think it would go with guava too well. Thanks so much for this recipe! I’m going to try it out again with buckwheat flour and see how that goes.
I made these yesterday and thought they were very yummy. I soaked for 8 hours using water and yogurt. Then I followed the rest of the instructions using 1/4 cup of maple syrup in place of sugar and added a mashed banana, some chocolate chips (enjoy life) and some leftover apple, spinach, and carrot pulp from my juicer. My kids love them and can’t even tell that they have fruit and veggies hidden inside.
Does it have to be wheat pastry flour? I have all kinds of alternative flours on hand. Namely rice and oat. Can I use one of them instead? I would mix xantham gum or other binder in with the flour. Would that interfere with the soaking/removing phytic acid? Thank you!
Nevermind, found it!
Do you have to rinse the water from your soaked flour? Are there any toxins leached into the water? Just curious.
Terrific! I did chia seed eggs because my littlest has an allergy unfortunately, and they turned out beautifully. I added cinnamon, (crispy) pecans and blueberries. Thanks you kindly for the great recipe!
This recipe is just excellent. I have made muffins and bread with it, and I add in a smashed banana and some strawberries – my kids love it!
They came out really addictive! I’ve already had 7 of them within 1.5h since they’re out of the oven. Must be the sugar! Now here’s a little about my try on this recipe: I used apples, but I cut them in small cubes and went a bit too far and cut up 2 cups, so decided I’d throw them in to make it more apple’ish. Unfortunately this increased the amount of the batter and I ended up filling 12 muffin cups + a glass pan 5x5inch. I didn’t use any spices, but I increased the vanilla extract to 2tsps, which turned out really well. Then probably because of too many apples I had to keep the muffins longer in the oven, about 30 minutes, which toughened some of the tops. The muffins also came out rather chewy, but I can’t figure if it’s from the apples or from the dough — the dough after soaking was pretty stretchy, is this normal in this recipe?
As for the sourness from acv, I could tell they were different than regular muffins but I didn’t mind it (the sugar enchanted me- I usually eat low-sugar and now I know why;) My husband however could tell it a bit more and despite the sweetness they reminded him of the soaked whole-wheat tortillas I had made last week (which btw. were pretty yummy, though sour.)
Here’s a question: If I decrease the acv to 1tbsp will the flour still soak the way it should and will this decrease the sour aftertaste in the muffins? Or if I use lemon juice instead of acv, will that improve the aftertaste?
Stretchy dough is normal after soaking.
You don’t want to decrease the acid as you need to keep the proper ratio in the recipe. Switching to another acid like lemon juice will adjust the flavor.
~Danielle, TCS Customer Success Team
Hi! Could this recipe be used to make loaf bread instead of muffins?
Yes, you can. You would need to bake it longer so that it is done in the middle.
~Danielle, TCS Customer Success Team