A Functional Medicine Cleanse, or Detox


This is how to do a cleanse from a functional medicine perspective. Sane. Grounded. Safe. Read the sister post to this, Detox Phases 1, 2, and 3.

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Want to do a cleanse but not sure how?

The ritual of a cleanse, purification, or fast, has been around a long time, spanning many cultures. Now cleansing and fasting are all the rage. There are lots of cleanses out there you may have heard of, including:

  • Fasting
  • Green juices
  • The old-school “master cleanse” (cayenne, maple syrup and lemon)
  • Ultra cleanses with powders as meal replacements
  • The liver / gallbladder flush
  • Special elimination diets

And many more! What does cleanse actually mean? On a physical level, it’s a temporary period of time when you do something intentionally to “purify” your body, or release stored toxins. Many approaches can work to activate the mobilization and removal of toxins. From a functional medicine perspective, there’s no one-size-fits-all approach. People are different, right? For example, liquid cleanses or fasts aren’t for everyone. Some people need food.

Back up, what do we mean by toxins?

This is worth understanding. The words toxin and toxic get thrown around a lot, but what do they really mean? What are you trying to get rid of? Generally, the word toxic means poisonous or harmful. Toxins come from inside and outside your body.

Internal toxins

In your body, these include:

  1. The byproduct of microbes that live in your gut
  2. Biotoxins like mold
  3. Damage from chronic infections like Epstein Barr virus or Lyme spirochetes
  4. Chronic inflammation
  5. Chronic stress chemistry
  6. Byproducts of your own cellular metabolism that don’t get efficiently processed and eliminated (like hormones or harmful metabolites of Phase 1 liver detox as explained in this post)
  7. Dead or damaged cells

If you do not have a perfectly functioning metabolism, no extra belly fat, no chronic inflammation or infections, spot-on liver function, and a perfect gut microbiome…. it’s likely you have some endotoxins to clean out.

External toxins

Most of these toxins come from your local pharmacy and liquor store! In other words, things you voluntarily ingest. External toxins also include pesticides, pollution, and metals like mercury and lead. Environmental toxins can get packed away in your body tissues, including fat cells.

Your body is constantly processing and eliminating toxins on a daily basis. However, it can be difficult to keep up with the load. That’s why it’s a great idea to do a focused detox on a regular basis – once, twice, or four times a year. How do you go about it?

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First of all, get elimination in order

As we discussed here, if you don’t produce at least one #4 Bristol stool per day, don’t go on a cleanse – yet. Why? You may create volatile, reactive, semi-processed chemicals that you will not be able to get rid of properly! This could mean reactive oxygen species (ROS or free radicals) that will cause inflammation and tissue damage. Also, the endotoxins from your gut can get reabsorbed, and cause widespread inflammation and pain.

If you’re not a good pooper, then check out dysbiosis, and address it first. You may also need to investigate food intolerance. Do these projects first before embarking on a focused cleanse.

Lighten your load

This means reducing your exposure to things that cause an added burden for your liver to process. You can do it these ways:

  • Don’t take unnecessary medications
  • Avoid the no-nutrition “substance foods” such as all added sugar, alcohol, and caffeine
  • Fast OR eat clean (more on these options below)
  • Lighten the load on your mind as well –– go on a retreat, a staycation, or just put up drama boundaries and lie low

Activate detox pathways

This is the fun stuff. You can design your own combination of foods and supplements to activate Phase 1 and 2 of liver detox. Or, you can use formulas that already exist, as most quality supplement and herb producers have good detox formulas. Also, fasting will activate detox pathways.

Don’t forget Phase 2! This is the phase that tends to be more sluggish and you do not want to activate Phase 1 without supporting Phase 2.

Choose Phase 1 and 2 activators from this sister post. Or, choose a formula. It’s essential to get all essential amino acids during a cleanse. Your liver needs all of them, in sufficient amounts.

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The why, how, and who of fasting


When you fast, even overnight, your body uses up your stored sugar (glycogen). This usually takes 8-10 hours. Afterward, you dig into your fat cells for energy, which releases toxins. It also turns on autophagy (pronounced aw-toff-a-gee), which is when your cells clean out debris. The longer you fast, the more time you have for autophagy. For those with GI microbial overgrowth, you’ll get more waves of your migrating motor complex (MMC) which is a sweeping out of your small intestine.


There are many approaches. My favorite is: fasting each night for 14 – 16 hours, a form of intermittent fasting (IF). This gives you up to 6 – 8 hours after glycogen is used up to dig into fat stores and promote autophagy and MMC action. You can also fast for a longer period of time as part of a cleanse, like 1 – 5 days. Get medical supervision for these longer fasts.

One fast I see great results with is the FMD (Fasting Mimicking Diet), which is five days, and you get to eat small amounts of food that keep you in autophagy without starving. It’s recommended to do the FMD once a month for three months, and longer for some conditions.


The types who do well with fasting are those who are:

  • Overweight or obese
  • Diabetic (but absolutely consult your doctor)!
  • Insulin resistant
  • Robust body types
  • People who are generally not stressed

Fasting does put you in a stressed state, but there’s evidence that you move beyond the stress after a certain number of hours. Hence, you need to be a person who can handle this. If you feel “hypoglycemic” – like you’re going to die if a meal is delayed, you actually could benefit from the metabolic reset you get from fasting, or it could be a bad idea. Consult your healthcare provider!

The who, why, and how of eating food


People are different. For some, it’s simply not a good idea to fast, or do liquids only. You will be better off doing a cleanse WITH food if you are:

  • Thin
  • Stressed
  • Insomniac
  • Have low fasting blood sugar
  • Get HANGRY with missed meals

If you’re in this group, the stress from going without food is not good for you. Why? Because the above signs indicate a strong likelihood of HPA-D, formerly called adrenal fatigue. Fasting/juicing and HPA-D do not mix. For your cleanse, do it with food.


  • You need a significant amount of amino acids for your liver to do its job. Amino acids come from breaking down your body (which you don’t need), or from ingested protein (preferable!).
  • You need fiber to bind with toxins and move them out through your colon. Fiber is in whole vegetables and fruits, however, it’s removed from juices.
  • Healthy fats are essential to stabilize your blood sugar.
  • Foods stimulate bile flow, and bile binds with toxins and moves them out.


  • Eat clean: Organic to avoid pesticides, and whole food to avoid additives.
  • Include protein: Half your ideal body weight in pounds – this is the number of protein grams to target, divided between “feedings.”
  • Add anti-inflammatory fats: Omega-3 fats from clean seafood, plus olive and avocado oils.
  • Combine glutathione with Omega-3 fats! This is important. Omega-3 fats are anti-inflammatory only if they don’t oxidize (think spoil) first. To prevent this, take glutathione, your body’s master antioxidant, with your Omega-3s.
  • Eat lots (7-10 servings) of organic fruits and vegetables per day for the nutrients and fiber.
  • Hydrate with decaffeinated fluids, aim for 60-70 oz per day, or 2 liters.
  • Add Phase 1 and 2 detox activators, such as selections from this post. The good news is that glutathione is key to activate phase 2.
  • Add fiber, to bind with toxins. Fiber also feeds beneficial gut bacteria and helps make good Bristol #4 stool.
  • Consider binders if you have gut dysbiosis, to bind endotoxins.
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Best veggies

The vegetables that provide nutrients for Phase 1 and 2 detox pathways include:

  • Crucifers (also called Brassica): Brussel sprouts, broccoli, cabbage, cauliflower, collard greens, kale, and turnips.
  • Leafy greens: Parsley, kale, watercress, chard, cilantro, beet greens, escarole, dandelion, and mustard greens.
  • Citrus: oranges, lemons and limes (avoid grapefruit and grapefruit juice, which slow Phase 1)
  • Sulfur-rich foods: garlic, onions (and eggs).
  • Liver and gallbladder supportive: Artichoke, asparagus, beets, celery, dandelion greens, arugula greens, and dandelion-root tea.

Lifestyle factors

While doing a retreat or staycation is idyllic, in reality, you can do a focused cleanse during regular life. Just pay attention to these lifestyle factors:

  • Wind down during your detox. You don’t want to detox while jacking up your stress hormones. Remember HPA-D and detox do not mix. So get your stress in order. Add restorative yoga, meditation, journaling, or infrared sauna time.
  • It’s also important to sleep well and enough. Eight hours per night is a minimum. Nine or ten is ideal. Give your body time to rest, clean and repair.
  • Move, move, move! Any movement is great, and sweating has an added bonus, as 1% of sweat is composed of toxic waste. Special caution here: If you have HPA-D, tone down exercise. Do move, but don’t overdo.

Special considerations for special people

  • Dysbiosis. If you wonder if you have dysbiosis, you can take a stool test prior. Tailor your detox to knock down bad microbes and build up good ones. Best test: GI Map.
  • Chemical toxins. Which toxins do you harbor? You can test for biotoxins, such as mold. You can also test for metals and various chemical exposures.
  • Detox capacity. What is the status of your body’s master antioxidant glutathione? Your levels of B vitamins? Your oxidative stress? Your detox pathways? Test these things with organic acids and blood work before embarking on a detox program.

Hopefully, this gives an idea of how to customize a cleanse. Want more help? Please, reach out!

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