Which SEEDS Should Be Soaked for Eating — and HOW {for nutrition, digestion and culinary purposes}

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I used to think that only the larger seeds and nuts needed soaking or sprouting before eating them. But the more I’ve learned about phytic acid, the more my eyes have been opened: High phytic acid exists in all seeds and nuts; and although it seems tricky to soak seeds like flax or chia, we’ll talk about easy solutions! Remember: Soaked seeds are more nutritious and gentle! You can read more about soaking and dehydrating both nuts and seeds, to make “crispy nuts” here, both how and why.

Which Seeds should be Soaked for Eating — and HOW {for nutrition, digestion and culinary purposes} #soaking #seeds #digestion #gapsdiet #paleo #soakingseeds #nutrition


What Do We Mean by “Soaked”?

We are not talking about making sprouts, like the alfalfa sprouts that used to be common on sandwiches, although the terms soaking and sprouting are sometimes used interchangeably; and soaking can be the first step of germination. Soaked refers to a soaking process that creates an enzymatic change within seeds. Dried seeds start out dormant, protecting themselves in nature from a potentially harsh winter. In this state, which is raw, seeds are indigestible and high in phytic acid. While health food enthusiasts tout the health benefits of eating raw nuts or seeds, they are misinformed. Our bodies can not access the seeds’ nutrition in their raw state, and the seeds wreak havoc on our digestive mechanism over time.

By soaking seeds in salt water, or another acidic medium, we are emulating or copying what happens in nature each spring. In spring, the soil becomes more acidic. This signals seeds to wake up and sprout, to no longer protect themselves, to send forth a shoot. Less protected from harsh, cold temperatures, means a reduction in phytic acid and less protection from our digestive mechanisms. Our bodies can easily digest a living vegetable instead of a dormant seed.

Occasionally, as with sunflower seeds, for example, you will actually see the germination or sprouting begin (which is the next step that naturally occurs from soaking); but our goal is the initial enzymatic process, and in most cases you will not see sprouts.

As I share below in more detail, seeds can be soaked in salt water, but they also transform in probiotic, acidic liquids, like kefir, yogurt, apple cider vinegar and sauerkraut juice. These mediums can all be used to make seeds healthier!

Which Seeds Need to be Soaked

Which Seeds should be Soaked for Eating — and HOW {for nutrition, digestion and culinary purposes}First off, the bad news: They all do, if eaten with any regularity or in any significant quantity.

Of course, small amounts of unsoaked seeds eaten only occasionally will probably not bother most people. But if you have leaky gut, any autoimmune issues or any kind of digestive or mental distress, including brain fog, please don’t hesitate to start some new “pre-digestion” methods. Soaking is worth the time it takes, and the methods become easy and automatic the more you do them.

Noteworthy: Seeds are often soaked by gardeners before planting. This trend gives us further insight: Gardeners soak seeds to get them ready to germinate, to signal to the seed that it’s time to start growing, imitating either the rains of spring or the wet acidity of an animal’s stomach. Gardeners want to ensure that their seeds will break their dormancy. This practical step tells us that seeds should be soaked. Soaking is what signals to a seed that it should become digestible, a living food.

Let’s discuss most edible seeds individually:


While very popular in health food circles, chia seeds do come wrought with phytic acid, phytoestrogens and insoluble fiber (source 1, 2, 3). Insert Sorry Face here. Yet, it’s true. When I use chia seeds NOW, as opposed to when I didn’t know, I use them as a tool (for example, a small amount in baking), and/or I ferment them first, which is like soaking, but more thorough: Fermenting is better and more effective at reducing the antinutrients in seeds.

Here are a couple of approaches:

  1. Sourdough: Make a baked good recipe, but add in a fermented product. This can be sauerkraut juice, kefir, yogurt etc. Make the recipe ahead of time, and allow it to sit at room temperature for 4 hours. Then put it in the fridge overnight or even for 2-3 days. This method works best when your original recipe already has some liquid that can be replaced by the probiotic liquid: Some water or milk in the original recipe gets replaced by the acidic medium or partially replaced; 1/4 cup of the acidic medium is usually enough to ferment the whole batter.
  2. Make a base ferment, similar to a chia egg: Instead of mixing water with chia seeds to make a chia egg (egg substitute), mix kefir, yogurt, sauerkraut juice or another fermented product with the chia. Allow it to sit at room temperature for 4 hours. Then put it in the fridge overnight or for up to 6 days. Use a scoop of this base in any of your recipes, instead of using raw chia seeds or chia eggs. (Use a blender to more easily incorporate them into your batter.) The seeds in the fermented base will be predigested to varying degrees depending on how long they culture. The ratio for a soaked (probiotic) chia egg is 1 tablespoon chia or chia meal mixed well with 3 tablespoons probiotic liquid. Larger batches of this kind of base can be made as well: 1/3 cup chia seeds to 1 cup probiotic liquid, for example.
  3. Make an overnight porridge by combining probiotic yogurt or kefir with chia seeds. Here’s an Overnight Chia Porridge recipe that uses this concept.
  4. Here’s a Grain-free Paleo Sourdough Bread recipe that uses the first method described above.


Similar to chia, flax seeds are tricky to soak because of the mucilaginous coating that happens when they get wet. Also, most of usWhich Seeds should be Soaked for Eating — and HOW {for nutrition, digestion and culinary purposes} are used to just throwing them into baked goods or smoothies. It’s hard to create new habits when old routines are deeply entrenched. But flax seeds should be soaked, and they are high not only in phytic acid, but also in phytoestrogens (source). So the more they’re predigested, the more balancing they become: less problematic to our hormone levels.

Best ways to soak or sprout flax seeds:

  1. Make your recipe using a fermented product. This can be sauerkraut juice, kefir, yogurt etc. Make the recipe ahead of time, and allow it to sit at room temperature for 4 hours. Then put it in the fridge overnight or for 2-3 days.
  2. Make a base ferment, similar to a flax egg: Instead of mixing water with flax, mix kefir, yogurt, sauerkraut juice or another fermented product with the flax. Allow it to sit at room temperature for 4 hours. Then put it in the fridge overnight or for up to 6 days. Use a scoop of this base in any of your recipes, instead of raw flax seeds or flax eggs. The seeds in the fermented base will be predigested. The ratio for a soaked (probiotic) flax egg is 1 tablespoon flax or flax seed meal to 3 tablespoons probiotic liquid.
  3. Here’s a great Butternut Squash Muffin recipe with which you can practice this method. Simply add 1/4 cup of probiotic food/beverage, and allow the batter to sit out for 4 hours. Then refrigerate overnight or for a couple of days, before scooping it into your muffin tin and baking!

Poppy Seeds

Poppy seeds are often ground and soaked for culinary purposes, to increase their flavor, or to add texture to a stew. (I used them here in a traditional Middle Eastern stew in this way.)

Poppy seeds are also unique because of their codeine/morphine content, which can actually affect the health and behavior of both kids and adults if eaten in large amounts, or if given to a baby. (source) Soaking poppy seeds in water for just five minutes, and then discarding the soaking water reduces their codeine/morphine content by 50%!

For the small amount of poppy seeds most of us eat, it’s not necessary, in my opinion, to reduce their antinutrients. However, if they’re allowed to ferment in any kind of a souring batter, that process will make poppy seeds more nutritious and certainly have a benefit, also making them gentler on our digestion. So if you can, do.

Hemp Seeds

For years I didn’t understand why the Weston A. Price Foundation discouraged the consumption of hemp seeds, until finally I was able to ask Sally Fallon herself, through a mutual friend. I got a good answer: polyunsaturated fats (source). Our bodies do not benefit from polyunsaturated fats (source), and hemp seeds are full of them. So really, we should eat hemp seeds rarely. When we do eat them, yes, they’re high in phytic acid, and they could be soaked in salt water, then rinsed, or put into a fermenting batter. See the section below on pine nuts and larger seeds for the salt-water method and ratios. Because hemp seeds are so small, they need a shorter soaking time of just two to four hours.

Sesame Seeds

Sesame seeds may be small, common and popular, but they also have a big secret: They are higher in phytic acid than any other food! Sesame seeds should always be purchased hulled, and/or they should go through some form of pre-digestion before being consumed. Otherwise, sesame seeds rob us of our nutrients. That’s what phytic acid does: It binds with minerals from our food and robs us of that nutrition.

Sesame seeds are also high in lignans, which are a class of phytoestrogens — They’re hormone altering, should not be eaten regularly or in large quantities and improve, like soy, through fermentation.

The easiest solution to both the phytic acid and the lignans in sesame seeds is to buy hulled tahini or hulled seeds, both of which have the majority of their antinutrients stripped off when the outer hull is removed. Sesame seeds or tahini may also be added to any kind of fermenting batter or fermenting nut puree (see how here) to improve their digestibility and effects on our health.

Mustard Seeds

For culinary purposes, mustard seeds should always be soaked first, because the one day minimum of soaking activates an enzyme— myrosine —that gives prepared mustards their distinctive flavor. (source)

Mustard seeds are comprised of 3% phytates. Rats fed mustard protein in lab studies became zinc deficient due to the excess of phytic acid (source). Of course, most of us don’t eat large amounts of mustard! But if mustard seeds are a staple in your diet, it’s noteworthy that they can cause a mineral deficiency.

If you plan to soak mustard seeds in water anyway, for culinary purposes, consider instead soaking your mustard seeds in salt water. This acid medium will further reduce phytic acid. Some mustard recipes will use apple cider vinegar for soaking; this is a good option too. You can even soak mustard seeds overnight in probiotic whey (the liquid drained from good quality yogurt) or probiotic pickle juice. Best yet is to make fermented mustard! Here’s a good, basic recipe.

Fenugreek Seeds

Perhaps surprisingly, fenugreek seeds, which we often see as an ingredient in curries, are very high in phytic acid (source). Fenugreek seeds, which have been studied quite a bit for their phytic acid content, are used medicinally for many conditions, including: digestive issues, blood sugar regulation, to reduce inflammation, to increase milk supply in lactating women, to increase exercise performance and to increase libido. Sprouting is a common way of reducing phytic acid in fenugreek; and it’s proven to be effective (source). Soaking has also been shown to increase the seeds’ nutrition and to reduce their phytic acid significantly (source).

Fortunately, we have no shortage of information on how to make fenugreek seeds healthier! Soak the seeds, ferment the seeds, put them overnight in yogurt or kefir, make a tincture with them using apple cider vinegar, put them in kombucha. Boiling and roasting the seeds also reduces their phytic acid, but not as much as soaking, sprouting or fermenting — just as we would expect! (source)

Pine Nuts, Sunflower Seeds, Watermelon Seeds and Pumpkin Seeds

Pine nuts, sunflower seeds, watermelon seeds and pumpkin seeds are all seeds that need to be soaked. Their soaking method mimics how we soak nuts: For every 4 cups of raw seeds, cover with room temperature, filtered water by two inches, and 2 tsp. sea salt.  Stir well to dissolve the salt.  Leave out overnight at room temperature to soak.  Drain them in a colander; and rinse them well. If you suspect old seeds, or possible rancidity, or mold, add 1/2 teaspoon vitamin C powder to the salted soaking water. This will kill any potential mold.

The seeds can now be dehydrated or used wet in recipes. Dehydrating and then carefully roasting these seeds further reduces their phytic acid.

Also, see my cookbook here, where these seeds are always soaked as part of the recipe. The cookbook features mostly nut and seed-based baked goods, prepared with predigestion in mind.

Other Seeds

Which Seeds should be Soaked for Eating — and HOW {for nutrition, digestion and culinary purposes}Technically speaking, all grains, legumes and nuts are seeds. Therefore, they all benefit from soaking. Most grains benefit from soaking overnight in a water and apple cider vinegar solution. Most legumes improve from a long soak in plain water; some need to be fermented. Nuts are best soaked in the same salt water solution outlined above for the larger seeds.

What about the tiny culinary seeds like caraway, cumin and fennel? These seeds are estrogenic, but historically have not been soaked; yet oils and extracts from these seeds have healing properties. So they are perhaps the exception to all other seeds (source). Of course, nobody eats very many caraway seeds; so any phytic acid they contain is somewhat negligible.  Pomegranate seeds are not soaked either.

One more recipe…

Here’s one more recipe for fermented (sourdough) batter. It’s a waffle batter recipe and gives you another opportunity to ferment your seeds, by providing a batter recipe that already incorporates the concepts discussed in this article. You can add your favorite seeds to the batter before it sours.

Are you more likely to soak your seeds in salted water or ferment your seeds in soured batter?

Comments 46

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  1. This is a fabulously detailed article. The best and most thorough collection of information and instructions for each type of seed, with examples, recipes, and options from soaking to fermenting. Thank you for all the work that went into compiling this information.

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      1. Thank you very much Maa`m for this useful information about soaking of seeds. I have one query. After we have soaked the seed say Flax seed over night , can we allow them to dry after draining water and then store them in some glass jar etc for use for a few days or they need to be consumed immediately on the same day. Would appreciate if you could enlighten us.

  2. This is so helpful! I’m especially grateful that you covered chia seeds and flax seeds. I love that porridge idea for the chia seeds, and the #1 tip for that too – such a good idea! Thanks for talking about the less talked about seeds like pomegranates and fennel. Great post Megan!

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      Researching this article helped me too, to see how far-reaching this issue is, and how it’s easy to let go of these methods, but it’s so rewarding to include them. Thanks for your comment, Renee!

  3. Hi Megan. Thanks very much for this. I make a linseed loaf by grinding the seeds into meal. Does it have the same effect to soak the meal in one of those mediums after grinding? If I soak the seeds beforehand they won’t grind well and I prefer the seeds ground for this loaf. Thanks!

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      Hi Antoinette, you’re welcome and great question! As long as you’re soaking the seed meal in a probiotic or acidic medium like ACV (not just salt water, in which case you need whole seeds, and they need to be rinsed afterwards), yes, that works! Meal, as opposed to whole seeds, can be soaked/fermented for an effective reduction of antinutrients! 🙂

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      Aw, Raia, I LOVE your honesty!! No discouragement needed! 😉 I think that’s my specialty: the bad news and then the good news!! Because I’d get overwhelmed too if there weren’t great solutions. So, yes, I make fermented hummus, for example! It’s easy and we LOVE it. Re tahini, the article mentions buying hulled; that’s the key point to start with! Buy hulled tahini; it’s not hard to find. Then proceed with your recipe, and ferment it if you can. Comment again with any specific recipe questions you may have, and I’m happy to try and help!! Re sesame seeds, I don’t soak them. I just buy hulled seeds (the white ones). And then I ferment them if I can. (But you could soak them…)

  4. What an informative post. So much gret information. I never really thought about soaking my seeds but after reading this, I will be doing so in the future. Thank you

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  5. What a great article Megan! I love that you have covered everything is such detail it is so helpful. I often soak in salt water but haven’t used fermented products. I am going to give this a try! I can appreciate the thought and time that went into writing this informative blog post so thanks for sharing, have pinned!

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      Thank you, Hope. I appreciate your kind words, and I’m so happy the article is helpful. I hope you enjoy the fermentation method. I find it the most exciting!! 🙂 Blessings!

  6. Sesame seeds and toasted sesame oil are used in small quantity in Asian cooking. For people who are allergic to these items, I’d say skip the seeds because they are mainly for decoration. Toasted sesame oil is mainly used as garnishing before serving a dish or used as marinade seasonings. Typically 1-2 tsp for 1.5 lbs meat. You can totally replace it with olive oil instead. There are many high quality sesame oil and sesame seeds made in Japan and are in excellent quality. Unfortunately they are pricy and hard to find in the US. Luckily I haven’t heard anyone addicted to sesame oil or seeds :))

  7. Such a great article! Thanks for such a comprehensive breakdown. I don’t always soak my seeds but now I’m thinking I should do it more!

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  8. Super informative article. Thank Megan. I confess I rarely soak or prepare seeds this way and perhaps it’s time to start. I don’t use a lot of seeds but appreciate the suggestions like the overnight Chia, for example, to incorporate the method, in the recipe itself! I will try both methods and see what works best for me.
    Q: When making fenugreek tea — are you suggesting people soak the seeds before making the infusion?

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      Hi Carol, thanks! I’m glad you’re considering soaking more often! In regard to soaking fenugreek seeds before making tea, if you soak them, you will be helping to release their fuller nutrition.

  9. Thanks for such a great detailed article, I really learned so much reading this! Hemp seeds were a surprise to me, had no idea I needed to soak them!

  10. I am confused about what to do with the water one uses to soak seeds like chia and flax. I grind chia and flax (one tablespoon of each) together and put it in the refrigerator over night. The next morning I drink the entire mixture as part of my IBS routine. Since reading your article, I am now questioning if that is safe to drink the entire mixture considering the phytic acid problem. I am familiar with soaking almonds to remove the phytic acid. With this process, I remove the almonds from the water, throw the water away and rinse off the almonds. Do I need to use a similar procedure with flax and chia?
    Thank you for all of this information

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  11. I want to eat chia seeds because of their omega 3. I’ve tried putting them in water in fridge overnight but couldn’t eat them they caused me pain. You can’t rinse them after soaking due to the gelatinous stuff they turn into. So, are you saying I can just put them In some plain Stonyfield yogurt for 4 hours at room temp and then in fridge and they would be fine like that? Does Stonyfield yogurt count as probiotic enough you think?
    Thank you!

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      Hi Jill, thanks for the great questions. Stonyfield yogurt does have a good probiotic count! So that’s good news. Yes, just what you said: You can soak your chia seeds in it overnight for reduced antinutrients. 🙂 Magical and easy! However, if unsoaked chia seeds cause you pain, it may be wise to find seed alternatives for a time. Not everyone should eat seeds (or nuts). Tigernut flour might be a better option to consider (https://amzn.to/2zIQLzy) And the best source for omega 3s, if you consume seafood, is virgin cod liver oil (here’s one in capsule form so you don’t have to taste it: https://bit.ly/2Li1Eg4). Best wishes!

      1. Hi Megan, I have a similar question as Mary’s – it’s not possible to throw out the water after soaking chia and flax because it becomes too gelatinous. I don’t eat yogurt (lactose) so is there another solution? And are you saying that the water/gelatinous “stuff” has the anti-nutrients in it so it’s not okay to consume chia and flax simply soaked in water? Or is it okay and if so, what makes it so? Thanks so much. Hope you can address this question!

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          Hi Robin, thanks for your questions. The soaking liquid for the seeds needs to be acidic (and will not be drained). The acidic medium will reduce phytic acid. You can choose from any non-dairy acidic medium: non-dairy yogurt, sauerkraut juice, water with apple cider vinegar added. This acid produces the enzymatic response for which we’re looking.

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  12. Hello, thanks for the informative article. I’ve always soaked my nuts and seeds, but not flax. For flax, I would grind the whole seed and then use, so do you recommend skipping the grinding part and just soaking as you describe? Or grind, then soak? Which is better? Thanks again.

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      Hi Kelly, it depends on what the whole recipe is and what the directions are after that step. Either approach is fine though. 🙂 Both will work, so whichever is easier, simpler. Or feel free to write back with more details about a particular recipe, and I can help you decide.

  13. Thanks for all the detailed tips. When I make a chia and flax porridge, I just soak them in almond milk for 20 mins before eating, so is it best to rather soak them in salt water (with or without a fermenting agent) and then rinse them and then add the almond milk before eating?

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      Hi Liezl, yes, that’s right: better to soak in salted water long enough for them to change enzymatically. But because chia and flax absorb so much it will be tricky to soak them without them taking on the flavor of whatever you soak them in. So not too much salt will be important I think. Then rinse and add your milk.

  14. Hi, thanks for the information. I’m soaking brown flax seeds in salt and vitamin c ascorbate, hoping the flax will be ”’supercharged” with vitamin c. How long should they soak, and should the mucilagenous water be rinsed off before making a smoothie?

  15. Hi thanks for theat useful information. I have a query about flaxseeds, I have been soaking and then fermenting (2 step process) and then using dehydrator to make flax biscuits. However I’m not sure if that is enough to get absorbed when I eat them as the seeds are still whole. wondered what you thought about this.

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  16. Hi Megan! I whole-heartedly agree with Robin Rainbow Gate – ‘best and most thorough collection of information and instructions for each type of seed’!
    Was hoping you might have a take on milk thistle seed? Not for recipes, just the preparation – any idea how to soak the seed but to then remove the -very bitty & tough when ground- bran?

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  17. Many sources online say that hemp seeds contain no phytic acid and don’t need to be soaked. They also supposedly have a good ratio of omega 6 and 3 fats, so I don’t see why they’d contain more polyunsaturated fat than other nuts and seeds.

  18. Many online sources say that hemp seeds don’t contain any phytic acid, and that they have a good ratio of omega 3 to 6 fats, so I don’t see why they’d contain any more polyunsaturated fat than other nuts and seeds.

  19. I used to believe the phytic acid soaking drill, but learned in the book “Understanding, Preventing and Overcoming Osteoporosis” by Jane Plant CBE, that it is a myth based on a limited study done long ago on a few puppies. She says phytic acid from these sources also has proven beneficial properties, so much so that it should be considered “Vitamin P”! Separately, I read a recent doctoral thesis from an Austrialian nutritional medical university program that tested if phytic acid was actually removed if nuts and seeds were soaked in water or salted water, whole or pre-ground. Turns out, soaking in either water or salt water does not remove phytic acid anyway unless the nuts/seeds are pre-ground in which case the nutrients are largely soaked out as well. I still soak whole nuts and seeds in water to germinate, but the phytic acid reason really doesn’t stand up when researched to its source.

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