So you’ve read my blog posts What Is CleanKeto, and Is CleanKeto For YOU, and you’ve decided that, yes indeed, CleanKeto is for you. Awesome! (And if you haven’t read those yet, please do so before deciding to proceed with CleanKeto…)

Whether you’re wanting to do CleanKeto for a few days for a quick cleanse and reset, for a few weeks to give your health and vitality a boost, or for a few months – or even for life – to experience all the anti-aging, disease-reversing, life-changing powers of CleanKeto, this Guide is your next step.

The purpose of this guide is to

  • get you started on the right foot with CleanKeto
  • help prepare you for the journey ahead
  • equip you with the tools and knowledge you need to get the best results possible for your efforts
  • and give you an idea of some of the challenges to watch out for and how to handle them when they do arise

Reading through this guide and doing all of the recommended steps (except for the grocery shopping and cooking) should take you only about an hour, total. So let’s dive in!

  1. Guidelines
  2. Mindset
  3. Measurements
  4. Support
  5. Plan Ahead
  6. Stock Up
  7. Clean House
  8. Cook
  9. Intermittent Fasting
  10. Begin!

Guidelines: A Quick Review

What is CleanKeto? Let’s do a quick refresher.

The basic guidelines are:

  • Paleo – whole, unprocessed, nutrient-dense ancestral foods (ie. pastured animal proteins, healthy fats, and whole fruits and veggies, and no grains, legumes, dairy, or artificial sweeteners, including erythritol and xylitol)
    • with the following refinements:
    • Anti-Inflammatory – to help quell inflammation and reduce the intake of gut-irritating lectins and phytates, and to improve your overall Omega 3:6 ratio, no nuts or seeds (or foods containing them, including nut butters and nut milks) are allowed, except for one handful of either whole macadamia nuts, hemp seeds, or soaked walnuts per day, max
    • Low Toxin – minimize your intake of toxins from food by choosing organic foods and drinking filtered water
    • Traditional Foods – Regularly add in bone broth, meats cooked bone-in, cultured foods, and/or sprouts to ramp up the nutrition and healing power another several notches!
  • Low Carb/Keto – 20 grams per day or less of carbohydrate intake (total, NOT net); stevia and monk fruit sweeteners are ok in very small amounts in very dark chocolate (>80%) and in foods such as soups, sauces, dressings, but not in beverages; all coconut products (oil, butter, milk, cream, flour, flakes) are allowed when eaten as part of meals – just make sure to keep within the <20g total daily carb allowance!
  • Clean Intermittent Fasting – 14:10 or longer every day (meaning, 14+ hours per day of clean fasting, and <10 hours per day eating window); “clean fasting” means no calories or flavors (except bitter) consumed outside of the eating window

CleanKeto is, at its core, an elimination diet, removing as many inflammatory and problematic foods, substances and influences as possible in order to speed healing, slow aging, reverse disease, and optimize health. Your foods will primarily be: pastured animal proteins, healthy fats, and low carb veggies and fruits. Most people find that within a few weeks – and often within just a few meals – CleanKeto significantly improves their energy, mood, sleep, digestion, blood sugar control, and hormone balance.

CleanKeto can be done for as little as one meal, and as long as a lifetime.

Note: Most people doing CleanKeto as a long-term lifestyle find that they get the best long term adherence and results with one of two approaches, either:

  • 90:10 or 80:20, meaning 80-90% on plan all of the time
  • or a cyclical 100% approach, meaning they alternate periods of being off plan with periods of 100% strict adherence to CleanKeto

If you find (like most people do) that you feel amazing with CleanKeto and want to make it your long term way of life, then I encourage you to experiment over time to find the approach that works best for your temperament, your lifestyle, and your mind/body/spirit.

My own personal example: over the past 15 years that I have been Paleo and low carb (and 7 years intermittent fasting), I have found that I only feel really great when I’m 100% on plan with CleanKeto. I can’t get away with 80:20 or even 90:10 – I just don’t feel good enough to stay on plan unless I’m all in. But with 100% CleanKeto, I feel like Wonder Woman. It is so awesome, it’s hard to believe it’s real. But no matter how good it feels, it is hard to maintain 100% adherence long term with all of life’s distractions and challenges, so I do 100% CleanKeto in regular spurts, aka Cyclical CleanKeto. This works really well for me as a way of life.

Mindset: Your BIG Whys

As you are getting started with CleanKeto, it’s helpful to get clear with yourself why you’re doing this – your really big whys. If you aren’t 100% sure yet of your biggest, most motiving whys, figuring them out will help you a LOT with staying on plan.

So, right now, take a few minutes and think about your big whys…

  • What is motivating you to want to make a big change?
  • What ailments are you suffering from that are holding you back from living your best life?
  • How will your life be different if/when these get better?
  • How do you feel about the mental and/or physical health problems that you are suffering from? (Note: These underlying emotions are often a real goldmine for motivation.)

Click on this image and hit Ctrl+P to print this out so you can make your notes:

When you’ve figured out your big whys, distill them down into just a few words that will be your touchstone in moments when you need a reminder of why you’re doing CleanKeto. Try to frame this as a positive thing to move toward, rather than a negative thing to run away from. Write your positive touchstone(s) in ALL CAPS.

Here are some examples from other CleanKeto-ers:

  • “I’m so sick and tired of being fat and not feeling good, and trying and failing over and over to lose the extra weight and get healthier. I feel so ashamed that I look like this. And I miss having pretty things to wear, that fit well. My big whys are that I want to be HEALTHY AND SLIM, and LOOK GOOD IN NICE CLOTHES. I’m willing to do whatever it takes, for as long as it takes, to get there.”
  • “Several of my family members have Type 2 Diabetes, and I’m scared to death of getting it myself. My big why is AVOIDING DIABETES and all the bad stuff that comes with it.”
  • “I’d really like to have a lot more energy, so I can do more, and enjoy my life more. I used to have so much more energy; being so sluggish isn’t me. The fatigue is really dragging me down, and making me feel bad about myself and unhappy with my life. My big whys are HIGH ENERGY and FEELING LIKE MYSELF AGAIN and LIVING A LIFE I LOVE.”
  • “I’m in pain every day. It’s so discouraging, and depressing, and exhausting. There are days when I’m not sure I want to keep living. If CleanKeto is going to help lessen the pain, I’ll do it, 100%. My big why is LESS PAIN.”
  • “My mental focus and ability to concentrate are deteriorating, slowly but surely. I feel like I have a cloud in my brain – it dampens my ability to think clearly, and I can’t remember stuff like I used to be able to, and like I should be able to. It’s messing with my job, and my mood, and my quality of life, and it’s damn embarrassing! And I’m scared about the future… What if it just keeps getting worse and worse? My big whys are I want my SHARP MIND back, and I want to AGE WELL – I don’t want to let this get any worse!”
  • “I suffer from depression and anxiety, and while meds help a bit, it’s still a major challenge to get through the day sometimes. I’d give just about anything to BE CALM AND HAPPY most days, and be able to GET OFF MEDICATIONS.”

Now, get a piece of paper and a marker, and write your touchstone words in ALL CAPS in big fat marker on that paper and post it somewhere prominent, as a frequent reminder for yourself. And I’d love for you to share them with me, too!

(Note: If you are already really clear on your big whys, and you’re ready to dive in, that’s fantastic! I highly recommend you do this quick exercise first anyway, to help cement that clarity.)


The next step is to find your baseline – your starting place – and then track changes over time, to help keep you encouraged and excited about your progress, and to help keep you on plan when the going gets tough.

If your goals are not body-centered, then you could skip this, but since positive changes are likely to happen with your body regardless of your focus, you might want to do this anyway, since these are a great indication of progress that can help you stay on track.

And, if you are slipping off track at any point, your measurements can give you some tough love (it’s hard to argue with a measuring tape – believe me, I’ve tried 😉), and inspire you to clean up your act again.

“That which gets measured gets improved”.

Get a cloth measuring tape (like this one) – or you can use a piece of string or rope and a metal measuring tape – and take the following body measurements, and write them down, with the date. Do this just before you begin CleanKeto, and then at regular intervals (at least weekly) while you’re on CleanKeto.

Calculating Body Fat %

One of the best measurements for determining overall health, and for tracking health improvements, is body fat percentage. So plug your measurements into this calculator to get a rough estimate of your body fat percentage:

The Zone Body Fat Calculator

Or, if doing math doesn’t float your boat, you can also get a pretty good idea of your body fat percentage from this image:

Recruit Your Support Buddy

One of the best ways to help guarantee your success with CleanKeto (or any new, challenging endeavor) is by having a support buddy, for numerous reasons:

  • to be accountable to someone other than yourself
  • to not feel alone in this endeavor
  • to encourage and be encouraged by someone else
  • to problem-solve with (or just to complain to, because venting is sometimes exactly what is needed!) when faced with challenges
  • to get creative with what to eat when you feel stumped or bored
  • and to talk you off the ledge when you’re about to face-plant into a bowl of chocolate pudding at the end of a hard day…

Your support person could be your romantic partner, a family member, a friend, a coworker, a neighbor – the only requirements are that they be 100% on board with you doing CleanKeto, and be accessible and responsive to you in times of need.

Now, the absolute ideal is someone you live with and share meals with, since having your support buddy right there in the house with you, and eating with you, is super helpful. And, clearing the house of off-plan foods really helps create success, and having the people you live with on the same plan as you is also incredibly helpful. But here in the real world, that’s just not always possible, for one reason or another. So…

The next best bet is a buddy who doesn’t live with you but is psyched to do CleanKeto right alongside you. Then the support is a 2-way street, and in helping each other stay on track, you also bolster yourselves. One great way to find your support buddy is to jump into my free Facebook group, “Dr Emily’s CleanKeto” – and connect with the members there. Friendly and supportive, everyone there is already at least somewhat familiar with and open to CleanKeto, and at any given time, there’s likely to be other members who are also looking for a support buddy themselves!

Plan Ahead

Planning and preparing ahead of time are also important keys to success.

Plan Your Timing

First, decide – how long are you going to do CleanKeto for, this time around? What’s appropriate for you depends on your goals, and on how much experience you have with low carb eating and intermittent fasting.


If you are just looking for a quick cleanse and reset, and/or you haven’t done low carb or intermittent fasting before, then start with just 3 days of CleanKeto to get a taste of it, and then duck out before you hit the roughest part, which is typically on days 4-5. [That’s when the body’s carb stores are running quite low (a good thing, and necessary for getting into fat burning mode), but fat burning hasn’t yet kicked in full blast, and so fatigue, cravings and other challenges are most likely to crop up.] This short stint will start training your body for longer runs later.


If you want to do a little deeper dive and get a bigger health boost, and/or you’ve done low carb and/or intermittent fasting before but it’s been a little while, then 1-2 weeks is a good timeframe for you, since that’ll get you past those hard initial days, get you into fat-burning mode, and get you starting to feel some real improvements. At that point, you can decide to keep going with CleanKeto, or take a break and then come back to it again (sooner rather than later!)


If you are wanting or needing some really powerful results and are ready for a really deep dive, and/or you’re an old pro at Keto and intermittent fasting, then you should opt for a longer stint – I recommend you aim for at least 30 days, so that you can begin to experience some of the real magic that CleanKeto has to offer.

Plan Your Menu

Regardless of how long you intend to do CleanKeto, planning your menu before you begin is also a must. Plan your menu for the full stint if you’re doing less than 2 weeks, and plan at least a week’s menu ahead if you’re going for 30 days or longer.

When looking through recipes, choose ones that either already fit the CleanKeto parameters or can easily be modified to fit them. Here’s a few to get you started:

[Want some more recipe options? Check out my ever-growing collection of CleanKeto-friendly recipes. And to be the first to hear about my latest recipes before they’re even published, subscribe to my weekly newsletter, “The Latest Goodies”.]

At least to begin with, aim to pick recipes that you already know and love that can be easily adapted to CleanKeto, so that your menu is comforting and enjoyable, and not too weird and unfamiliar and challenging. (Unless you are an adventurous cook and eater, and thrive on variety and trying new things. In which case, have fun with it!)

What are you likely to do? Tried and true, or adventurous and new? Share your plans! 

Once you’ve got your CleanKeto recipes picked out, plug them into one of these menu planners:

Stock Up

And now it’s time to shop! I love food shopping… Do you? If so, have fun with this! If not so much… well, then, keep it simple and get it over with quickly. 😜

Stocking your pantry, fridge & freezer full of CleanKeto-friendly foods that you look forward to eating is another essential key to success. I can’t stress the importance of this enough! You need to be prepared ahead of time, so that when those moments come (and they will come) when you want something quick and easy (and possibly off-plan) and you just don’t feel like cooking anything, you don’t have to! You can just grab something you (or someone else) prepped ahead of time and chow down, and in a few minutes, you’ll feel much better, without having nose-dived into something naughty. 😉

The CleanKeto foods that will work for you to have on hand to keep you satisfied and on-plan are very personal – some people love olives, or avocados, for instance, and they totally do the trick, and some people hate them. Figuring out which foods will work best for you might take some time, and that’s fine. The important thing is to keep at it until you find your CleanKeto happy foods. Once you do, the whole thing gets a whole lot easier.

A Note on Snacks

The ultimate goal with CleanKeto is no snacking – before, between or after meals. But when you are first getting started – and even for the first few months, while you are working on training your body to become an awesome fat burning machine – you will likely need CleanKeto-friendly snacks (= high in protein and/or fat, and low in carbs), and you should absolutely have them, as often and as much as you need them, to keep you from getting hungry, cranky and/or tired (because that way lies disaster!)

Some examples of quick CleanKeto-friendly snacks are: olives, guacamole, hard boiled eggs, pork rinds, jerky, cocoa nibs, very dark chocolate, a small handful of macadamia nuts or soaked walnuts, or unsweetened toasted coconut flakes.

Ok! Printed menu plan and recipes in hand – it’s time to make your grocery list, and go do your food shopping!

Clean House

Welcome back! How was your grocery shopping trip? 😜

Now that you’re all stocked up on all sorts of CleanKeto goodies, it’s time to remove all off-plan foods from your house.

Your chances of success are much higher if there’s nothing off-plan within easy reach, and instead, all that’s near to hand is on-plan CleanKeto foods. If you hesitate to do this housecleaning step because you hate to throw food away, I completely understand! Here’s what to do about that:

If you’ve got healthy foods that just aren’t CleanKeto (ex. Paleo-friendly foods that are not low carb), then either wait to start your CleanKeto stint until you’ve finished them up yourself, or if you’re ready to start CleanKeto now and don’t want to lose your momentum, then give them to a family member or friend, either for them to use, or for off-site storage while you’re doing CleanKeto. Or donate them to a food bank. Win-win!

And if they’re not healthy foods, then they’re not good for anyone and are better off in the garbage anyway. But if you know people who will want to eat them regardless and you really don’t want to just throw them away, then give them away. But either way, get them out of your house!

Foods to remove from your house at least temporarily:

  • all dairy products except for butter and ghee from pastured animals
  • legumes (this includes all beans, dried peas, lentils, and peanuts, and all foods that contain them)
  • keto sweeteners from sugar alcohols (erythritol, xylitol, maltitol, etc.) and foods containing them
  • off-plan fruits and veggies (ie. high carb)
  • nuts and seeds (except macadamias, hemp seeds, and soaked walnuts)
  • nut milks and creamers

Foods to remove from your house permanently:

  • all grains and products containing them (bread, pasta, crackers, cookies, chips, canned soups, sauces, etc.)
  • highly processed “vegetable” (seed) oils and all products containing them (read labels carefully! these super unhealthy oils are everywhere – for more on this topic, see my article “The Best and Worst Vegetable Oils”)
  • highly processed foods of any kind – if it comes in a box and/or is in the middle aisles of the supermarket, it is probably trouble
  • artificial sweeteners (Splenda, Aspartame, etc.)
  • CAFO meats
  • non-organic fruits and veggies, especially the most heavily sprayed ones


Now that you’re stocked up, take a couple of hours and make as much of your food ahead of time as you can – at least a few days’ worth, and even a few weeks’ worth. Batch cook soups and stews and freeze extra portions for later use, prep sauces, dressings, and seasoning mixes, wash and chop veggies, etc. If you balk at taking this time now, just think of the time it will save you later, and dream about how wonderful it will be when mealtimes roll around and your yummy, healthy CleanKeto foods are all prepped and ready for you to enjoy, no fuss, no muss! 😄

Your Progress So Far

At this point, you’ve already made a bunch of progress in your CleanKeto journey! You’ve:

  • delved into and posted your big whys for doing CleanKeto
  • measured your bod and recorded the results
  • got your support buddy on board
  • decided how long you’ll be doing CleanKeto this time around
  • planned your menu
  • gone grocery shopping
  • stocked your pantry, fridge and freezer full of yummy, happy-making CleanKeto foods that you’re looking forward to eating, and
  • cleaned out your house of off-plan foods

Way to go, you! 😊

Intermittent Fasting

The final big piece of CleanKeto is clean intermittent fasting (IF). Whether you’re an old hat at IF, or have never done it before, or somewhere in between, this part’s pretty easy in the scheme of things (way easier than giving up some of the foods we’re eliminating!), and pays major health dividends.

Wherever you’re starting from, your goal is to get to at least 14 hours of clean fasting per day, which means your daily eating window – from your first ingestion of calories of the day to your last – is less than or equal to 10 hours. This is called 14:10, and that’s step one.

Then, step two – go farther if you can, to 15:9, and 16:8, then to 17:7, 18:6, and even 19:5. The longer your daily clean fasting period (up to 19 hours), the more fat-burning and healing you’ll be doing, lengthening your body’s natural state of clean-up and rejuvenation, called “autophagy”.

[Note: I don’t recommend going shorter than a 5 hour daily eating window without personalized guidance from a knowledgeable health care practitioner, because of the powerful effects this can have on your hormones (not all of them positive, esp if you have thyroid issues!) If you want to try out an eating window of 4 hours or shorter and don’t have a practitioner to guide and monitor you, then only do it occasionally (no more than twice per week, and never for 2 or more days in a row), and carefully monitor how you feel, before, during and after, and stop at the first sign of any adverse effects, including – but not limited to – fatigue, insomnia, anxiety, or low mood.]

There are a few ways to accomplish shortening your eating window and lengthening your fasting window:

  1. Shorten your eating window by just a little bit each day – for instance, start eating 15 minutes later each day, and/or stop eating 15 minutes earlier each day, until your eating window is just 10 hours, then 9 hours, and so on.
  2. Start by removing all carby calories from your mornings, and instead have only protein and fat before Noon (don’t change your eating schedule at all, yet). This will help reduce your insulin production, calm carb cravings, and level out your blood sugar. Once that is easy and has become habit, then work on shortening your eating window.
  3. If you are feeling bold, and/or have some experience with low carb and/or intermittent fasting, go directly to clean 16:8 or even 18:6, and then alternate with longer eating window days as needed. You’ll know it’s needed if you wake up insistently hungry in the morning, carb cravings intensify, you get cranky mid-day, or you can’t seem to get enough to eat in the evenings despite stuffing your face.

If you are aiming to do CleanKeto for longer than just a few days’ reset, and you (like many people) do better with taking on only one major change at once, then you can choose to start this intermittent fasting “training” portion first, before you do the rest of CleanKeto, and wait until you’re comfortable doing at least 16:8 daily before beginning the other parts. Or, you can do the food part first, and work on implementing the fasting later. As I like to say to my patients all the time, Rome wasn’t built in a day! The important thing is to begin, and make progress, in whatever way you can.

You are now well on your way with your CleanKeto journey, and are retraining your body to be a serious fat-burning machine, reducing inflammation, improving body composition, energy, mood, blood sugar and hormone balance, and slowing aging and reversing disease.

I’d love to hear from you about how CleanKeto is going for you – share when you begin, how long you plan to continue, and your challenges and successes and inspirations along the way!