Microbiome Rebuild Phase

By Phase 3, digestion should feel more stable and food tolerance slightly improved. This phase focuses on increasing nutrient diversity, supporting microbial balance, and gradually expanding foods that help restore gut resilience.

This shopping list provides a practical starting point for building simple, repeatable meals.

Protein Sources

Choose clean, minimally processed options.

• Chicken
• Turkey
• Salmon
• White fish (cod, haddock, pollock)
• Tuna (in water)
• Eggs (if tolerated)
• Tofu
• Tempeh

Vegetables

These form the foundation of most meals.

• Broccoli
• Cauliflower
• Kale
• Spinach
• Cabbage
• Bok choy
• Carrots
• Celery
• Mushrooms
• Green beans
• Snow peas
• Sweet potato
• Pumpkin
• Butternut squash
• Zucchini
• Artichokes
• Beets
• Eggplant
• Cucumber

Antifungal Vegetables (Introduced in Phase 3)

These vegetables are commonly included during this phase because they contain compounds associated with supporting microbial balance.

• Onion
• Garlic
• Leeks

Introduce cooked first to assess tolerance.

Fruits

Fruit should still be used in moderate amounts.

• Banana
• Pear
• Papaya
• Honeydew melon
• Avocado
• Berries (small portions)

Whole Grains

• Oats
• Brown rice
• Quinoa
• Millet
• Buckwheat
• Amaranth

Seeds & Fibre Sources

• Ground flaxseed
• Chia seeds

Nuts & Nut Milks

Allowed:

• Almonds
• Almond milk
• Tigernut milk

Avoid in this phase:

• Cashews
• Cashew milk

Healthy Fats

• Extra virgin olive oil
• Coconut oil
• Nuts and seeds
• Nut or seed butters (single ingredient)

Functional Foods

• Spirulina tablets
• Sea vegetables (kelp, nori, wakame)

Drinks & Hydration

• Filtered water
• Alkaline water (optional)
• Herbal teas

Tea (Encouraged During Phase 3)

• White tea – up to 3 cups daily
• Chamomile tea (evening)

White tea contains antioxidants and is traditionally associated with supporting detoxification and circulation.

Example Phase 3 Pantry

Many people find it helpful to keep a small collection of reliable staples.

Examples:

• olive oil
• coconut oil
• herbs and spices
• brown rice
• quinoa
• flaxseed
• spirulina
• herbal teas

Keeping meals simple reduces decision fatigue and supports digestive consistency.