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Ketosis versus Autophagy: What’s the difference?

This is a great question I got in one of my live Q&A sessions that I thought was worth further exploration. What is the difference between ketosis and autophagy? First, let’s start with ketosis. Ketosis is a state of healing that signals your body is burning fat for energy.  This is why most people come to fasting and the ketogenic diet, for weight loss. But there are so many other amazing health benefits to ketones. Ketones travel up to the brain and enhance neurological healing. Ketones increase GABA and calm the brain. Ketones also have an anti-inflammatory effect on the body. 

How do you get into ketosis?

Well, the answer to this question will vary for each person, depending on their unique composition. However, what we do know is that ketosis kicks in when blood sugar goes down, and usually 13-15 hours of intermittent fasting will push the body to make the switch from burning sugar to burning fat. When the body realizes that you’ve run out of sugar to burn for energy, it will instruct the liver to make ketones. However some people may need to fast a little longer to get into ketosis. Measuring your ketones with something like a Keto Mojo will ensure you know whether you are in ketosis or not. Alongside fasting, you’ll also need to stabilize blood sugar by counting macros, reducing carbohydrates and increasing good fats. 

Now, let’s shift to autophagy fasting. What is autophagy?

Autaphy is a natural, regulatory mechanism inside the cell that instructs the body to clean out damaged cells, in order to regenerate newer, healthier cells. Autophagy helps clean up the mitochondria and everything inside the cells, as well as bad bacteria. Best of all, autophagy can initiate cell death, also called apoptosis, when sick cells commit suicide by activating an intracellular death program. Now, something important to note is that autophagy is not always a signal of fat burning. So ketosis and autophagy have different healing purposes, and can be happening at different times or in parallel. 

How do you get into autophagy?

Research is showing that autophagy kicks in between 17-72 hours. The key to autophagy is keeping protein low. Whereas in ketosis, we try keeping protein under 50g, with autophagy fasting, we try to stay under 20g of protein. Note that introducing food may kick you out of ketosis, but it may not kick you out of autophagy. 

There is one commonality that affects both ketosis and autophagy, and that is toxicity. Toxins like BPA plastics, phthalates, heavy metals, fluoride, endocrine disruptors will jam up receptor sites for glucose and insulin. When this happens it becomes difficult for people to bring down blood sugar, keeping people from getting into ketosis. 

When cellular death happens and the person has a high toxic load, the toxicity can prevent the cells from getting properly cleaned up and removed from the body, instead they get redistributed, causing a variety of uncomfortable symptoms like rashes, brain fog, weight gain, etc. So the thing to remember here is that a high toxicity can make the autophagy fasting process uncomfortable. 

What are you trying to accomplish?

If you’re trying to figure out whether to go for ketosis or autophagy fasting, think about what you are trying to accomplish. If you are trying to burn fat, lose weight or get the brain benefits of ketones, ketosis might be the better fit. In fact, you might want to start with the 5-day KETO CALM Fast Training Week.

On the other hand, if you are trying to detox and prevent disease, autophagy may be the better fast for you. Listen to The Resetter Podcast episode with Naomi Whittel, where we talked about how to heal yourself with autophagy, foods that stimulate autophagy and how autophagy affects sleep. 

Finally, can you be in both ketosis and autophagy at the same time? Yes! While being in ketosis does not automatically mean you’re in autophagy, if you’re fasting longer than 17 hours and you’re keeping protein down, you might be in both ketosis and autophagy.

If you’ve got more great questions for me, join me in my weekly LIVE Q&A sessions on YouTube, every Thursday at 11am PST.



  1. Timothy Houlton November 20, 2020 at 2:15 am - Reply

    Would love a copy of beginners guide to fasting if possible, thanks!

  2. maylee iwai May 17, 2021 at 9:34 pm - Reply

    OKAY, looks like we can induce both ketosis and autophagy at the same time if we fast >17hrs and maintain <20g protein. But what about the other macros, carbs and fats?

  3. Daisy Hays September 26, 2021 at 6:52 pm - Reply

    So we can be in Ketosis without being in Autophagy. But can we be in Autophagy without Ketosis? I don’t see how.
    I have done Keto three times for >6 mos each time, and all three times is it has made my PMDD worse (unbearably), so Ketosis is actually bad for me. Does this mean I can’t do fasting, since fasting induces Ketosis?

  4. Donna Lindsay October 2, 2021 at 1:08 pm - Reply

    Beginners guide please

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