What to Take During Eating Windows: My Fasting Supplement Protocol

A 38-year-old software engineer came to my telehealth practice last month—she'd been doing 16:8 intermittent fasting for six months, lost 12 pounds, but hit a wall. "I'm exhausted by 2 PM," she told me. "My workouts feel terrible, and honestly, my hair's thinning." Her labs showed what I see all too often: borderline low magnesium, vitamin D at 28 ng/mL (optimal is 40-60), and electrolytes that looked like she'd run a marathon in the desert.

Here's what I wish someone had told her earlier: when you're fasting matters almost as much as what you're taking. Get the timing wrong, and you're basically throwing money—and potential benefits—out the window.

What the Research Actually Shows About Fasting and Nutrients

Look, I get it—fasting feels simple. Don't eat, get benefits. But your body's nutrient needs don't pause just because you're not eating. In fact, some needs increase.

A 2023 meta-analysis in Nutrition Reviews (doi: 10.1093/nutrit/nuad007) pooled data from 14 randomized controlled trials with 1,247 total participants doing time-restricted eating. They found something fascinating: people who fasted without attention to micronutrients had 37% higher rates of subclinical deficiencies (95% CI: 28-46%) compared to those who ate normally. The biggest gaps? Magnesium, zinc, and B vitamins.

But here's where it gets really interesting—and where most people mess up. Dr. Rhonda Patrick's work on nutrient timing shows that taking fat-soluble vitamins without dietary fat reduces absorption by up to 50%. A 2022 study in the American Journal of Clinical Nutrition (2022;115(4):1092-1103) had participants take vitamin D3 with either a high-fat meal (30g fat) or on an empty stomach. The high-fat group had 32% higher serum levels after 12 weeks (p=0.002).

And magnesium? A 2024 randomized controlled trial (PMID: 38456789) of 312 adults doing 16:8 fasting found that those taking magnesium glycinate WITH their evening meal reported 41% better sleep quality and 28% less muscle cramping compared to taking it while fasting (p<0.001 for both). The empty-stomach group? Let's just say digestive complaints were... notable.

What to Take When: My Clinical Protocol

Okay, so here's exactly what I recommend to my fasting clients—and what I do myself on 16:8 days.

With Your First Meal (The Nutrient Power Hour)

This is when you load up on nutrients that need fat or protein for absorption:

• Vitamin D3: 2,000-4,000 IU with food containing fat. I use Thorne D/K2 because it includes vitamin K2 (mk-7)—critical for directing calcium to bones, not arteries. The European Food Safety Authority's 2023 assessment confirmed safety up to 4,000 IU daily for adults.
• Omega-3s: 1,000-2,000 mg EPA/DHA combined. Nordic Naturals Ultimate Omega is my top pick—third-party tested and consistently pure. Take with food to prevent fishy burps (yes, even the good brands can cause this on an empty stomach).
• Fat-soluble vitamins A & E: If you're taking these separately (most multis include them), take with food. Retinyl palmitate for A, mixed tocopherols for E.
• CoQ10: 100-200 mg if you're over 40 or on statins. The ubiquinol form absorbs better but costs more.

With Your Last Meal (The Recovery Stack)

This is about setting up your body for the fasting period:

• Magnesium glycinate: 200-400 mg. The glycinate form is gentle on digestion and promotes relaxation. Pure Encapsulations Magnesium Glycinate is what I keep in my own cabinet. Avoid citrate at night unless you want multiple bathroom trips.
• Zinc: 15-30 mg of zinc picolinate. Zinc supports immune function and protein synthesis—helpful since you're not eating protein overnight. NIH's Office of Dietary Supplements notes the upper limit is 40 mg daily from supplements.
• Protein powder if needed: If you struggle to hit protein goals, a clean whey or plant protein here can help maintain muscle during fasting. I like NOW Foods Whey Protein Isolate—no fillers, third-party tested.

What About During the Fast?

Honestly? Mostly nothing. True fasting means water, black coffee, tea. But if you're doing longer fasts (24+ hours) or feel terrible:

• Electrolytes: Sodium, potassium, magnesium in water. But here's the catch—most commercial electrolyte mixes have sweeteners or calories that break autophagy. I tell clients to make their own: 1/4 tsp salt (sodium), 1/4 tsp NoSalt (potassium), and magnesium powder in water.
• B vitamins: If you must, sublingual B12 (methylcobalamin) won't break a fast. But honestly? Just wait for your eating window.

What drives me crazy? Companies selling "fasting support" supplements with branched-chain amino acids (BCAAs). BCAAs spike insulin—they literally break your fast. A 2021 study in Cell Metabolism (doi: 10.1016/j.cmet.2021.03.011) showed that just 5g of BCAAs raised insulin 37% in fasting subjects.

Who Should Be Extra Careful (or Skip Fasting Altogether)

Intermittent fasting isn't for everyone, and supplements won't fix underlying issues:

• Pregnant or breastfeeding women: Just don't. Nutrient demands are too high. The American College of Obstetricians and Gynecologists explicitly advises against restrictive eating patterns during pregnancy.
• People with adrenal fatigue or HPA axis dysfunction: If your cortisol is already dysregulated (often shows as afternoon crashes, sleep issues), fasting can make it worse. I've seen this backfire too many times.
• Those with eating disorder history: This should be obvious, but I'll say it anyway—fasting can trigger old patterns.
• People on certain medications: Diabetes meds, blood pressure drugs, lithium. Fasting changes how your body processes these. Always, always talk to your prescriber first.
• Anyone under chronic stress: If you're going through a divorce, working 80-hour weeks, or caring for a sick parent? Now's not the time to add metabolic stress.

My software engineer client? We adjusted her timing—magnesium with dinner, vitamin D with avocado breakfast—and added a quality multivitamin (Thorne Basic Nutrients III). Within three weeks, her energy stabilized, and those 2 PM crashes disappeared. Her 3-month follow-up labs showed vitamin D at 42 ng/mL and magnesium in optimal range.

FAQs (The Questions I Actually Get)

Q: Can I take my multivitamin while fasting?
A: Depends on the multi. If it has fat-soluble vitamins or minerals like iron, take it with food. If it's just B vitamins and vitamin C, you can take it fasting—but you'll absorb the Bs better with food. Honestly? Just wait for your eating window.

Q: What about collagen during fasting?
A: Collagen has calories (about 40 per scoop) and contains protein. Technically breaks a fast. But if you're fasting for weight loss rather than autophagy, it might be okay. For true autophagy, skip it until you eat.

Q: Do I need extra supplements for autophagy?
A: The best autophagy booster is... fasting itself. A 2019 review in New England Journal of Medicine (2019;381(26):2541-2551) found that most "autophagy supplements" (like spermidine, resveratrol) have weak evidence in humans. Save your money.

Q: How do I know if my electrolytes are off during fasting?
A: Muscle cramps, headaches, dizziness, heart palpitations. Start with sodium—1/4 tsp salt in water often fixes it. If symptoms continue, break your fast and reevaluate.

Bottom Line

• Time your supplements with your eating window—fat-soluble vitamins (A, D, E, K) and minerals need food for proper absorption.
• Take magnesium glycinate with your last meal to support sleep and prevent cramps during fasting hours.
• Avoid "fasting supplements" with BCAAs, sweeteners, or calories—they likely break your fast.
• If you feel terrible while fasting, it might not be about supplements—reevaluate if fasting is right for you right now.

Disclaimer: This is educational information, not medical advice. Always consult your healthcare provider before starting any new supplement regimen, especially if you have health conditions or take medications.