When Exercise Recovery Becomes Harder to Handle: Troubleshooting Root Causes


Within the autoimmune community, I’ve heard many people talk about a decreased ability to recover from exercise. “I can’t do my workout like I used to,” “I take twice as long to recover,” “I’ve had to stop running.” It’s frustrating when, in addition to the symptoms you live with daily, you can’t handle the physical activities that bring you joy.

I don’t have a degree in exercise science. However, I love exercise, I live with autoimmunity, and I have successfully transitioned from complete inactivity back to an active life. The transition was slow, the path indirect and frustrating, but every step toward recovery was worth it. Those days of wondering if I’d ever go for a hike again feel far away, yet I know they are just around the corner if I treat my body wrong; it’s my job to take great care of my body so I can continue to do the activities I love.

Along the way, I’ve made some mistakes and learned some hard lessons (and cool facts!) about how autoimmunity and exercise go together. My goal in this article is to give you some tools for troubleshooting the root causes of why exercise recovery becomes harder to handle, so that you can continue with, or return to, the activities you enjoy.

If you’re having a hard time recovering from your workouts, you may notice some of the following symptoms:

  • inability to complete workouts
  • decline in performance
  • need for naps or serious rest after workouts
  • loss of general motivation and enthusiasm
  • depression
  • irritability or aggression for minor reasons
  • weakened immune function
  • loss of menstrual cycle
  • unexplained change in weight
  • sleep disturbances
  • increased leaky gut symptoms

The Outside-In Approach

There are various reasons for a change in exercise recovery. As with any bio-hacking project, I like to approach it from an outside-in perspective: First, rule out the factors that sit outside of your body, such as lifestyle habits, sleep, and diet, then move inward to consider internal factors such as micronutrient deficiencies and other physiological issues. The internal factors can take more energy and sleuthing (and expensive medical testing!), so it makes sense to rule out the simpler options first.

Based on this outside-in model, below is a list (top-to-bottom, from outside-in) to use when trying to suss out your situation:

Avoidance: This one won’t apply to most readers, but ought to be mentioned. For a lucky few who don’t have physical deficiencies and are rock stars at diet and lifestyle habits, avoidance of overtraining is the only thing needed; train with mindfulness and you won’t have recovery problems. But they won’t be reading this. With that said…

Overtraining: First try to figure out if you are simply overtraining. How? Back off your workouts significantly, and if you find your recovery goes back to normal, continue with a reduced exercise program and watch out for signs of overtraining. “More is better” isn’t always true. And remember to allow enough recovery time between workouts. Overtraining is the direct route to many of the symptoms listed above, and it’s relatively easy to remedy.

Another approach: Switch from one exercise mode to another. For example, quit CrossFit to take up moderate aerobic exercise, or kick your running habit to try High Intensity Interval Training (HIIT). Not everyone responds well to every type of exercise, and sometimes a mode-switch is all your body needs. Yes, each type of exercise has its special benefits, so switching gears may mean modifying expectations, but which is better: doing the alternative that allows you to work out in some fashion, or not being able to work out at all because your exercise of choice is too much for your body? If backing off or switching modes doesn’t help, move to the next step: diet.

Exercise causes the body stress. That’s part of how it strengthens us; our muscles exert themselves and the body repairs the “damaged” muscle. If all goes well, the repaired muscle will be stronger than before. Net: If exercise causes too much stress, exercise less.


Inflammation: Are you on an anti-inflammatory diet? Reducing inflammation is key for living well with autoimmunity, and helps with exercise recovery.

Insufficient calorie intake: Are you eating enough calories to handle your workouts?

Insufficient protein intake: Are you eating enough protein to help your muscles rebuild and allow your body to do its regular duties? The U.S. RDA of 0.8 grams per kilogram of lean bodyweight (1 kilogram = 2.2 pounds) per day is inadequate for most people who are very active, recovering from illness, or depleted (think: autoimmunity). If you’re active, you might do better with 1-1.5 grams per kg. I’d collapse on the 42 grams of protein per day that the RDA recommends for me!

Insufficient carb intake: Are you consuming enough carbs? For many AIP and Paleo types, low-carb is the status quo, however, consuming too few carbs can have various detrimental effects, as summarized in this article by Paul Jaminet. If you are low carb, consider going higher carb to compensate for your exertion. Note: Many people start AIP needing to be low carb, and once the body starts to heal, a higher carb diet is necessary.

Hydration: Are you dehydrated? Try to consume at least half your body weight (lbs) in ounces of water per day, more with strenuous exercise. Most athletes are mindful of hydration during exercise, but maintaining hydration afterward is important, too. Your pee should be clear to light yellow; if it’s dark, you’re dehydrated.

Sleep: Adequate sleep is critical for recovery from exertion. Most of us don’t get enough to even handle a normal day, much less a workout. What is so important about sleep? Among many factors:

  • During sleep, we produce HGH, or Human Growth Hormone, an important hormone for tissue repair and regulation of metabolism.
  • Lack of sleep increases cortisol production, which can increase risk for digestive issues, depression, memory impairment, exhaustion and weight gain.
  • During sleep, the liver completes vital detoxification.
  • Lack of sleep increases systemic inflammation; inflammation drives the autoimmune process.

Deficiencies/Genetic Mutations: Micronutrient deficiencies and MTHFR are common with autoimmunity, are related to many of the symptoms we live with, and can underlie reduced exercise recovery. Each topic below warrants an article of its own; here I’ll list some common issues, and encourage you to look into them with your doctor if you find the above suggestions don’t fix your recovery problem. Don’t be surprised if you have more than one of these issues. They are all resolvable with time, patience and smarts:

– red blood cell anemia
– ferritin anemia
– Vit D deficiency
– Vit B12 deficiency
– depressed adrenal function
– MTHFR and associated mutations
– histamine intolerance
– SIBO and leaky gut

6 Added Tips for Making the Best of It

Autoimmunity or not, there is no one recipe for the “perfect” exercise routine, because every single body has unique needs. Figuring out why you have reduced ability to recover can take some time. Be patient, and look at it from all angles:

  1. Stress: Are you managing your life stress in order to ease the load on your body?
  1. Medical: Do you have a doctor who is willing to do necessary medical testing and help find the root causes of physical issues?
  1. Self-Education: Are you empowering your healing path by reading up about autoimmunity and related factors?
  1. Support: Do you have a solid support system? If not, how can you manifest one?
  1. Track It: Keep a daily journal or chart of when you exercised, how long you slept, what you ate, and life stressors. If you find yourself feeling drained, you might see a relationship between factors.
  1. Take It Slow: It’s better to back off and stay healthy than to over-do it in an effort to meet a milestone. If you push it, you may pay the price of having to back off for a few weeks or even months.

At whatever level you can, create room for exercise in your daily routine – whether it’s a treadmill desk, a walk around the block with the dog, gentle yoga, a jog in the woods or CrossFit. When you make time for exercise, you may find it creates more energy for other things.

Whether you’re figuring out a decrease in exercise recovery, or returning to exercise after a long break, expect to have some setbacks, and use them as learning moments to help gauge your path forward. Then, as you begin to resolve the factors that are holding you back, you should be able to increase your exertion level bit by bit. Next thing you know, you might be returning to yoga class or calling a friend to accompany you to the gym.

To end, an apropos quote from Mark Sisson:

“The human body is resilient, but there are limits – and the limits aren’t always clearly delineated. To divine them, it takes finesse and thoughtful tinkering at the edges. Sometimes you have to fall off the edge to know where it is. It’s more art than science.”

About Susan Vennerholm

Susan Vennerholm is the blogger behind Backcountry Paleo, where she shares AIP-specific recipes and autoimmune-friendly tips for backcountry enthusiasts. She also geeks out on the medical side of autoimmunity, and loves to write about it. Susan wholeheartedly believes that self-education and networking in the AI community are two of our strongest tools in living successfully with autoimmunity. As a way to pay forward the support she received during her recovery, she blogs so that others will have more resources for their healing journey. A certified yoga teacher, code wrangler, and freelance writer, Susan loves climbing mountains, watching Orca whales, trail running, volunteering for dog rescue, and a good fantasy novel. You can connect with her on Facebook and Pinterest.


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