Natural Yeast Trouble-Shooting (UPDATED June 2, 2013)

UPDATE: Nov. 2015: See my new Youtube videos on how to use natural yeast!

Copyright 2015 Caleb Warnock. Images and text may not be used anywhere without written permission of the author. This blog content is not in the public domain. Short quotations with link and attribution are permitted. 

[picture: pizza at our house made with natural yeast dough]

Hello world :)

Hundreds and hundreds of you have gotten free, non-sour natural yeast starts from me and Melissa, who is my co-author on The Art of Baking with Natural Yeast: Breads, Pancakes, Waffles, Cinnamon Rolls and Muffins. We give starts away, at no cost, to anyone who asks for them in the U.S. and Canada. If you want one, go here:

We believe our cookbook is the first natural yeast cookbook to be published in the U.S. in more than 60 years, and the book is being called “ground-breaking." Natural yeast flattens the glycemic index, takes away heartburn and acid reflux forever, helps prevent or reverse gluten intolerance and, in some cases, full-blown Celiac’s disease, turns natural phytic acid into an anti-oxidant, controls allergies, and turns flour into a yeast that is both pre-biotic and pro-biotic. Natural yeast is amazingly healthful and free -- I know it sounds like a multi-level marketing pitch, but yeast was invented by God and has been used to make bread for more than 6,000 years -- until we traded natural yeast for synthetic, laboratory created yeast in 1984 (I've now learned that yeast was genetically modified even before 1984.) 

Many of you have emailed me to say how much you love baking with the natural yeast, and we are grateful for that. Some of you have emailed with questions and struggles.
There is a learning curve to using natural yeast. It is very different than the laboratory-created yeast that has been in grocery stores since 1984. But with a little instruction, natural yeast quickly becomes easy to use. Once you have gotten your free dried natural yeast flakes from me, here is what you do:

Step 1: Trust the process! The yeast you get from me will be a tiny "dust" or "powder" or smashed flakes. Some of you have been concerned that you are not getting "enough" -- but hundreds if not thousands of people have now successfully used this "dust" to start yeast. So don't panic when you see how small the amount is. It will come in a see-through plastic packet. Pictured on a spoon, it will look something like this:

[picture: natural yeast flakes on a spoon]

Step Two: In a jar, mix the flake "dust" to a quarter cup of lukewarm water and a quarter cup of flour PLUS one heaping teaspoon of flour. I use fresh-ground whole wheat. You can use whatever you want.

[picture: flour and water mixed with yeast flakes)

Step Three: Let this sit on counter for two days. At the end of two days, you may or may not see visible bubbles. Either way, don't worry.

Step Four: Add 3/4 of a cup of lukewarm water and a cup of flour to what is in your jar. Let it sit on your counter until you see bubbles, which could be in a few hours or may take a day, depending on temperature etc. 

However, if you DON'T see bubbles after 24 hours, remove half of what is in your jar and add 3/4 of a cup of warm water and a cup of flour to what is left in your jar. This time, MAKE TWO CHANGES:

Change One: Use water a bit warmer than you used last time. 
Change Two: Warm the jar periodically (once an hour is preferable). You can do this in several ways. You can turn your oven on its lowest setting for about one minute, then turn it off and put your jar inside. Or you could lay the jar in a crockpot and turn it on low for a minute and turn it off, leaving the jar in side. Or lay your jar in a toaster oven on warm, turning the heat off after about a minute. Or even put your yeast jar inside a bowl of warm water for a couple minutes. Whichever of these steps you choose, repeat about once every hour or two, until you get bubbly yeast.

If, after 12 hours, you still don't see bubbles, repeat this step again until you do. DO NOT put your yeast in the fridge. I've gotten letters and emails from some of you who are not seeing bubbles after the first grow-out, and you are putting your yeast in the fridge. Don't do this! Putting it in the fridge slows the growth down tremendously! Remember that yeast is a living thing, and must be fed to be happy and grow. Just keep repeating step four until you see bubbles, using slightly warmer water each time (but never scalding hot!). And remember, if there is a layer of liquid on top of your yeast after it has sat four 24 hours, you are not using enough flour! When you feed it next time, increase your ratio of flour to water.

[Click here for Caleb's Edible Weedkiller Recipe!]

If you DO see bubbles, your yeast is ready to use! 

However, because it has been out on the counter for so long, it is likely beginning to go sour. Here's how to make it go "sweet":

Step Five. Scrape the yeast from the jar, until only a residue remains. See photo.

[picture of the same jar of yeast, with yeast removed, and only a residue remaining.]

Step Six: Wash about half the residue out of the bottle and let it go down the drain.

Step Seven. Put a half to three-quarters of a cup of lukewarm water into the jar. Swirl it around to mix the water with the remaining residue of yeast. Remember, you want to grow it out with as little of the original yeast as possible, because this is what will keep your yeast sweet and new.
[picture of water mixed with a small residue of yeast.]

Step Eight. Add flour until you have a shaggy mass of dough.

[picture of the same yeast and water, this time mixed with flour to form a shaggy mass of dough.)

Step Nine. Let this sit on your counter for 12 hours, until is has visibly risen and has lots of bubbles, like this:

[The same yeast, 14 hours later. Notice the pockets of bubbles]

Step Ten. if there is still any hint of sourness, repeat steps 5-10.

Step Eleven. Now cook or bake. And when your jar is empty (because you used your yeast to cook or bake), repeat steps 5-11 again.

NOTE ONE: If you have not used natural yeast before, I STRONGLY suggest you start by making pancakes or waffles, because those are much easier than homemade bread, and it will give you chance to get a feel for working with your new natural yeast start. 

NOTE TWO: Once you have turned your flake dust into bubbly yeast, the easiest way to keep your yeast sweet is to grow it in the fridge. I do this by following steps 5-8 above, and then instead of letting it sit out for 12 hours, I let it sit out for an hour or two, and then I put it in the fridge. After a day or two in the fridge, the yeast will begin to rise. The yeast can be left in the fridge for up to a week.
common questions:

Q: The sample of natural yeast you gave me was dead.
A: Some of you have emailed me to say that the sample yeast I gave you was “dead”. First, let me say that I use the exact same yeast flakes to start my yeast. The flakes I gave you are from exactly the same batch of yeast that I use. And my flakes grow out every time. This should prove that your flakes are not “dead” but perhaps you need more help in learning the process of growing out natural yeast from flakes. If kept cool and dry, natural yeast does not die, ever, in its dried flake form. I repeat, natural yeast DOES NOT DIE, EVER, in its dried form. We know this because yeast flakes from the tombs of Egypt have been reconstituted and grown out. I have check this out -- it is a fact and not an internet rumor. When yeast is dried, it goes into stasis, which means that it is in long-term hibernation. It can be slow to wake up. Be patient, careful and exacting in following directions. If you threw out your sample because you thought it was dead, never fear, you can get another free sample by email m e at

Q: My yeast has turned brown.
A: You have used too much water. THIS IS THE MOST COMMON CAUSE OF SO-CALLED “DEAD” YEAST. I cannot emphasize this enough. If your flour and water mixture was soupy, you did not use enough flour (see recipe above). Water is heavier than carbon dioxide. Carbon dioxide is what yeast creates to makes its bubbles. When natural yeast is mixed with flour, it (literally) eats the tannins, lignans, and glutens, and produces “bubbly yeast” as a by-product. If you have a soupy mix to begin with, the yeast grows out, the weight of the water squeezes the carbon dioxide bubbles out, and the yeast NEVER looks bubbly even though it has grown out. You can always tell if your mixture was wrong (soupy) because a layer of water gathers at the top of the yeast. This water has a brownish tint, due to oxidation of the yeast.
If you had “dead” yeast that had a layer of brown water on the top, you used too much water. To fix it, take a teaspoon of yeast from the center or bottom of your "brown" yeast jar and follow steps 5-10 above.

Q: Since it is easier to start with live yeast instead of dried yeast, can I get some live yeast from you?
A: You can. I ship live yeast FREE with seed orders of $15 or more from my seed website, This is the website where I sell my guaranteed-pure, never hybrid, never GMO vegetable seed. Check it out :)

Q: How do I make a backup dried yeast?
A: To make flakes from live yeast, use this recipe:

Step One: Put a piece of wax paper the size of a cookie sheet on your kitchen counter.

Step Two: Put a quarter-cup of wet natural yeast (at peak rise -- don’t use old yeast) in the middle of the wax paper.

Step Three: Put another sheet of wax paper over the top of this. You now have a sandwich of wax paper and yeast. Use your hands to squish the yeast between the sheets of wax paper. Pull the sheets apart and put them, (face-up, of course) on the racks in your oven. Do NOT turn the oven on. They go on the oven just to keep the wet yeast away from stray floating hair or flies or anything gross that you don’t want in your yeast. Leave the wax paper in the oven for one to two days until completely dry. If you don’t squish the yeast very thin, or if you use more than a quarter-cup, the yeast could take up to A WEEK to dry, so follow the recipe carefully if you want dry yeast in one to two days.

Q: (from an email to me) "Can I get a start of your yeast that you offered in your blog post? I actually got a start from you before, but it developed mold on it so maybe I let is sit out too long."
A: UPDATED ANSWER: Let me just say that when I originally wrote this post, here was my answer: "Natural yeast does not go moldy.  It cannot because of the acid content. This is documented in our new cookbook." I assumed that people who were complaining of mold were actually seeing what the break-making world calls this the "brain." (see below). But then, in the spring of 2013, one day I ran out of flour and was in a hurry and I grabbed some whole wheat pastry flour I had purchased, and I used it to grow out my yeast, and the next day, the jar was filled  with disgusting mold! I could not believe it. This is the first time I've ever had mold in my natural yeast, ever. So now I guess I can't say natural yeast doesn't go moldy! So don't use pastry flour. I suppose this is also possible with white flour, but I don't know because I don't use white flour (because it is metabolized by the body exactly as though it is white sugar -- very bad for you). It has also been pointed out to me that perhaps natural yeast could go moldy in places with high humidity. I live in a very dry desert, so I suppose this is possible. At any rate, if you get real mold (and not just brown water or a brown "brain" layer, as explained below) then take that dried yeast back-up that you created (you did, right?) and use it to start over again. That is what I did.

Now, about the "brain." I hate that term. Not exactly a term of art! Anyway, it means that the top of your yeast has gone brown. This is because natural yeast oxidizes, exactly the way a cut banana turns brown, or an apple, or a potato. It is NOT  mold, and it is not dangerous. It does mean your yeast has gone sour. You can still use a teaspoon of this yeast in the recipe above to re-sweeten your yeast.

Q: My bread is a brick! Help!
A: A couple of answers. First, when adding yeast to a recipe from our cookbook, use yeast at or near peak rise. This will help. Second, the kneading is ENORMOUSLY important. So...

Tips for kneading BY HAND: Knead 250 times by folding the dough in half. Then, let the dough rest for 20 minutes. Then knead another 250 times. Then let the dough raise.

Tips for kneading BY MACHINE: Use the lowest gear possible. For example, on the Bosch, use setting one only. Knead for five minutes. Then turn off the machine and let the dough rest for 20 minutes. Then knead for another ten minutes, and let it raise.

If you are having trouble, here is a brand-new recipe for bread:

(copyright 2013 Caleb Warnock. This recipe MAY NOT be shared in any way without express written permission.)

This recipe makes one loaf.

Step One: Put 1 1/3 cups warm water in a large bowl.

Step Two: Add ONE TABLESPOON of natural yeast, one teaspoon honey, one tablespoon olive oil and stir.

Step Three: Add three cups whole wheat flour, and one cup of bread flour and 1/2 teaspoon salt. Stir with a Danish dough hook (or with your hand) until just incorporated.

Step Four. Begin to knead the dough by hand, folding firmly in half 250 times.

Step Five. Let the dough rest for 20 minutes.

Step Six. Knead another 250 times.

Step Seven: Place dough in greased and floured bread pan. Warm the jar periodically (once an hour is preferable) FOR SIX HOURS. You can do this in several ways. You can turn your oven on its lowest setting for about one minute every hour. Or you could put the pan in crockpot if yours is large enough and turn it on low for a minute and turn it off, leaving the jar in side. Or put your pan in a toaster oven on warm, turning the heat off after about a minute. Or even put your loaf pan inside a casserole dish of hot water for a couple minutes every hour.

Step Seven. After six hours, your bread will have risen some, but may not have doubled. Don't worry about it. Simply put that loaf pan in the oven on 400 DEGREES for ten minutes, then reduce the temperature to 350 degrees and bake for another 30 minutes. Enjoy!

Thanks everyone! -Caleb


  1. If you buy two copies of the book, you can get free shipping. I am buying an extra to give as a gift along with a start of the yeast - it's not too soon to be thinking about Christmas!

  2. Very helpful! Thank you, Thank you!

  3. THANK YOU for putting this information out there! May God bless you for all the work you've done and provided!

    I got impatient waiting on my start of natural yeast, so I experimented with using my homemade kefir to ferment my bread dough. It's been a fun experiment, with fairly good results! I just got my yeast flakes yesterday and started growing them out today, I'm so excited to embark on this journey!

  4. Love both books! Thanks for sharing the information on natural yeast.

  5. Hello:
    By all means correct me if I'm wrong, when you stated "We believe our cookbook is the first natural yeast cookbook to be published in the U.S. in more than 60 years, and the book is being called “ground-breaking” by our publisher." I was wondering if that is right because I have a book called Tartine Breads by Chad Robertson which I have been following and experimenting with for a year now. There is also a "Tartine Bread Experiment blog that I follow and use. So does this still apply to your comment?
    Thanks for all of your work, dedication and for the two books which are a frequent page turner in my daily life as well.

  6. hi there! for problems with your wild yeast, look here...



    1. This is so cool! I ran to Macey's to get some dark rye flour to try your starter method. I currently have a Pioneer starter I've been using for twenty years plus a San Francisco and a new starter from South American grapes I purchased at Walmart.

  7. I followed these directions exactly and after doing all the steps through 9, I had no bubbles. What should I do?

    1. did you use fresh ground wheat flour or flour from a bag? i literally have been 100% successful in creating 'something' using fresh ground wheat. mind you until i realized too much water was causing my problem what that 'something' was was generally foul and cause for frustration.

  8. interesting...after this step...

    In a jar, mix the flake "dust" to a quarter cup of lukewarm water and a quarter cup of flour PLUS one heaping teaspoon of flour. I use fresh-ground whole wheat. You can use whatever you want.

    I wonder just how much of your yeast actually remains and how has grown from the native yeasts in the freshly ground wheat. before buying your book and before reading i would generally create something foul...after the book, after this blog entry I have been extremely successful - the key here? don't use too much water. it will cause a problem..

  9. I have some bubbles, it looks and smells good but it DOES NOT expand!!! I have tried the troubleshooting method from the book and it still does not increase. Suggestions??!!!

  10. A question:
    As the start is sitting "on the counter" for a couple of days at the beginning, does it matter that the room is relatively cool? We keep our thermostat @ 60-65 degrees in winter. Maybe I should put it under a warm light or something to give it a little more warmth?

    1. no, this shouldn't make a difference. it will take (bit) longer...

  11. Still working on my start 3 days later...
    I'm a bit confused by your instructions on this site vs. what is in your book. Nowhere does the book say to wash everything down the drain every cycle and start over with just a 'dirty' jar. Did I miss something?

    1. from my experience this only necessary the first time you want to use the yeast you have created or when the mixture has become less than the desired flavor (and you want to sweeten it up). i have personally been doing this about every 6-8 weeks when the yeast begins to loose is vigor or when the yeast starts to yield bread that doesn't taste good.

  12. I used the pineapple juice technique with success. My natural yeast starter is going well, and I've made a few batches of bread with it.

  13. Do not used softened water (or chlorinated water)
    Like others who have commented I just couldn't get mine to come close to doubling in size. It smelled good, bubbled, and I followed directions exactly but each time I repeated steps 5-9 it got weaker and eventually had no activity. So I ordered flakes from a recommended place in the book and their instructions specifically said to not use softened or chlorinated water. Turns out that was all I was doing wrong.
    I hope my failure helps someone else avoid my mistake.

  14. How long does it take to get a response from the email requesting a free start? I bought the book......

    1. Wow - fast reply. Thanks for the link Caleb. Maybe the 2nd edition of the book can have a shortcut barcode or something...

  15. Am having results with the natural yeast - adapted my old wwbread recipe using coconut oil, raw honey, eggs, ww flour, 3 cups starter, and less water than originally called for - bread looks wonderful, has an amazing texture, tastes so good, and feels so good and satisfying. Have avoided gluten for 20+ years, but feel wonderful and am sleeping better. I have 7 daughters, 3 sons, and taught each of my girls at age 7 to grind and make ww bread thinking they were getting 100% of the nutrition - now I am having to train my daughters and dil how to do it properly with natural yeast. Just made Melissa's wonderful coco blueberry cake for our empty nester home evening group tonight, and it is fabulous. Made my frosting with coconut cream and semi sweet dark choc chips. Put some green choc chips - for St Patricks and blueberries on top and am so pleased with the results. Taught a class to nine local ladies last week, after doing some intense experimenting and learning and had a great response. Shared some dough ready to put into loaf pans and made more dough for the ladies to learn the method and take some home. They have all gone out bought your book which I highly recommended. The info is all so incredible and definitely promotes God's way as opposed to man's way. Can't thank you enough. It feels so much more fulfilling as a homemaker.

  16. meant to say - having fabulous results

  17. Ok, I began my start on Friday. In the book it says to dissolve flakes in the water and then add 1/4 cup of flour. I used freshly ground wheat. The book also says to put it into the fridge immediately after mixing this concoction. Today (Mon) I looked again at my start and...... nothing....... I looked online at the blog and the directions are completely different. The book says that if I have a sluggish start to set in out on the counter for no more than 2 hours. I have done that and nothing still.....
    Not sure what to do at this point?

  18. I got my flakes and mixed them with water then flour. Overnight I had bubbles and a little bit of brown liquid on top. I decided to go ahead and feed the starter with 3/4 cup of water and flour. Within 8 hours or so it had doubled in size and is very bubbly! But... now what?! Is it sour... should I scrape it out and leave a residue of starter to "sweeten" it? I'm almost giddy of my success. My husband thinks I'm nuts. :)

  19. I bought your book, sent for your flakes twice and both times they died. I tried making my own starter from scratch - it died. In every case I got a few bubbles the first day and it was downhill from there. A few days ago, I read where water filtered with reverse osmosis will not work with natural yeast. The yeast needs minerals. LIGHT BULB!!! I switched to bottled spring water (our city water has chlorine and flouride - I will not consume it). Now after 2 days, I am getting bubbles!!! This tip may be somewhere are you site or in the comments and possibly everyone knew it but me -- I need to share it for anyone not having success. I may finally get to bake with natural yeast! So excited!!! YEAH!!!!

  20. I bought the book, sent for the flakes twice, but have yet to receive anything. I'm willing to blame the Hawaiian postal service--heaven knows it's failed me before--but I'd really like to get started. It's been over six weeks since the second letter should have arrived. Any ideas on other sources for natural yeast? The other one mentioned in the book now charges way too much.

  21. I have tried twice to get a start going with my flakes. Both times I left it on the counter after adding warm water and WW flour. Within a day there only a couple bubbles but has a layer of brown liquid. Should I feed it if it is forming the liquid or should I just leave it for the full 2 days undisturbed before feeding it again?

  22. I got mold on the top after 2 days. Threw it out! What did I do wrong?

  23. Could you please tell me what bread flour is? Is it a refined flour? I don't want to use anything that is refined. If it is a healthy flour, could you recommend a good source for it? I have a mill and would prefer milling from organic berries if possible. Thank you

  24. Hi,
    I need some help! I received my live starter from Caleb on Monday, right away I did what the book said. I am having issues, do you happen to have the instructions on what do to with the live yeast once you get it. Thanks!

    1. This comment has been removed by the author.

    2. We have been working with our live starter for over a week. It didn't end well for us either. At first we were getting the brownish water on the top. We removed a few teaspoons to put 1 tsp in a few different jars to try different water to flour ratios. After 12 or so hours they either stayed a shaggy mass of dough or if they had more liquid it would have the brown water on top again.

      We do have chlorine in our tap water so we used our carbon filtered refrigerator water and tried bottled water with the same result.

      We finally killed them all one when after the first 12 hours. I took one of the dryer ones and added a little more water and mixed it and waited another 12 hours. The result after 24 hours was mold in all of the jars.

      We live in the humid free AZ desert?
      We are using freshly ground hard red wheat?

  25. This comment has been removed by the author.

  26. I need instructions for the live yeast please.

  27. Thank you for the recipe for the bread. Everything is looking right but I am getting a brick too so the tips are helpful and I am going to try the recipe. Thanks!

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