Basic Soaked Muffins – with Video

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soaked muffins
Inspired by Millie’s master muffin recipe, and because I have a need for a good soaked basic muffin recipe, I joined Millie in tweaking and playing with muffins. And I think I’ve got a good, basic muffin recipe now! Thank you, Millie, for your great example, pioneering spirit, and inspiration. 😀

My favorite muffin spice is ginger. In these muffins, it tastes a little bit lemony. So I think adding some poppy seeds to the soaking would be a really nice addition. I’m going to try that next time.

Soaking grains is very important – the step of soaking neutralizes the phytic acid, which, if left unchecked, would block mineral absorption. You might also be interested in the Basic Sprouted Muffin, which uses sprouted flour. Sprouted flour offers the benefit of phytic acid being neutralized, but it also offers additional benefits: it digests like a vegetable, and certain vitamin levels are increased.

Makes 1 dozen muffins

  • 1-1/2 cups whole wheat pastry flour
  • 1/2 cup rolled oats
  • 2 tablespoons raw apple cider vinegar or Kombucha
  • 1 cup raw milk
  • 2 local, pastured eggs
  • 1/2 cup evaporated cane juice or Sucanat or other solid natural sweetener (powder in food processor if coarse)
  • 1 teaspoon vanilla
  • 1/2 cup virgin, unrefined coconut oil (melted if solid at room temperature)
  • 1 teaspoon sea salt
  • 2 teaspoons aluminum-free baking powder

Spices of your choice: (I like…)

  • 2 teaspoons cinnamon
  • 1 teaspoon ginger
  • 1/4 teaspoon nutmeg

Add-ins of your choice: (I like…)

  • 1/2 cup raisins
  • 1/2 cup chopped crispy nuts (soaked, then dehydrated ala Nourishing Traditions style)
  • 1/2 cup unsweetened shredded coconut
  • 1 cup shredded zucchini, apple, or carrot (additional moisture may require additional cooking time)

In mixing bowl, combine flour, rolled oats, apple cider vinegar (or Kombucha), and milk. Cover and let soak overnight, up to 24 hours.

When ready to bake, preheat the oven to 375 degrees.

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.

soaked muffins 2

Add wet ingredients to the soaked flour mixture. Mix until smooth.

Add add-ins and mix to incorporate.

Fill oiled muffin tin, or paper-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 gently browned.

Take out of oven and transfer muffins to a cooling rack. Store in an airtight container when fully cooled.

This post may contain affiliate links. We only recommend products and services we wholeheartedly endorse. Thank you for supporting Traditional Cooking School by GNOWFGLINS with your purchases. Our family thanks you!


  1. says

    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! =-.

    • says

      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!

    • says

      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.

    • says

      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.

  2. Kim says

    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.

    • says

      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!

  3. Susanna says

    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?

    • says

      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.

    • says

      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!

  4. vanessa says

    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?


    • says

      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!

  5. Susanna says

    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. :)

  6. 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.

    • says

      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!

  7. says

    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)
    5g protein

    I’ve got my flour soaking now…. can’t wait to bake the muffins (and eat them!)
    .-= Shelly @´s last blog post… Getting Ready for Muffin Goodness =-.

  8. 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!

  9. 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!

  10. Josefina says

    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.

    Tusen tack!

  11. says

    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.

  12. Sharon says

    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

  13. julie says

    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.

  14. Shinies says

    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.

  15. Wendy says

    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.

  16. Carla says

    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!

  17. Selina says

    Do you have to rinse the water from your soaked flour? Are there any toxins leached into the water? Just curious.

  18. Rachel says

    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!

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