Cooking From Scratch: The First Step in Any Gut Health Protocol

If there’s one habit I recommend before any supplement, any elimination protocol, or any expensive gut microbiome test, it’s this: cook from scratch. Not because it’s trendy, or because it makes for pretty photos — but because what you cook, and what you leave out, has a direct, measurable effect on the trillions of microbes living in your gut.

As a doctor and gut health coach, this is the foundation I build every client’s plan on. Before we talk about probiotics or protocols, we talk about the plate. Let’s get into why — and exactly how to start.

Why cooking from scratch is a gut health strategy

Your gut microbiome is shaped, meal by meal, by what passes through it. Every ingredient you choose is either feeding beneficial microbes or disrupting them. This is where cooking from scratch stops being a lifestyle choice and becomes a clinical one.

When you cook at home, you control three things that matter enormously for gut health: what’s in your food (fibre, polyphenols, whole ingredients your microbiome recognizes), what’s not in it (preservatives, emulsifiers, excess sodium, seed oils, artificial additives), and how varied your ingredients are across a week — which, as I’ll get to, may be the single most underrated lever for microbiome diversity.

Packaged and ultra-processed foods work against all three. Research linking ultra-processed food intake to reduced microbial diversity, increased gut permeability, and low-grade systemic inflammation continues to grow — and this isn’t a fringe finding anymore. It’s one of the most consistent threads in gut microbiome research today.

Ditch the processed foods — including the “healthy” ones

This is where I want to push back on something I see constantly, even among health-conscious families: the “healthy” processed food trap.

Protein bars marketed as clean. Gut-health yogurts loaded with added sugar. “Veggie” chips that are mostly potato starch and oil. Plant-based meat alternatives with a longer ingredient list than a candy bar. These products are formulated to look like the healthy choice on a label, while still containing the same emulsifiers, gums, artificial sweeteners, and industrial oils linked to gut lining disruption and altered microbial balance.

A useful rule I give clients: if a food needs a marketing claim to convince you it’s healthy, be skeptical. Whole foods don’t need a health halo — the ingredient list is the claim.

Practical swaps I recommend:

• Trade packaged granola bars for homemade energy balls (dates, nuts, seeds — nothing else needed)
• Trade flavored yogurt for plain yogurt with fresh fruit
• Trade bottled salad dressings for a 3-ingredient olive oil, vinegar, and mustard vinaigrette
• Trade stock cubes and packet sauces for a simple homemade stock or sauce base you batch and freeze

None of this requires being a chef. It requires reading labels and defaulting to ingredients you recognize.

Fiber: the nutrient your gut microbiome is starving for

If I had to name the single most important nutrient for gut health, it’s fiber — and most people, even health-conscious ones, aren’t getting nearly enough.

Fiber isn’t just about “regularity.” Specific fibers — particularly the fermentable kind found in vegetables, legumes, whole grains, fruits, nuts, and seeds — are food for your gut bacteria. When your microbiome ferments fiber, it produces short-chain fatty acids like butyrate, which help maintain the gut lining, regulate inflammation, and influence everything from immune function to mood.

Cooking from scratch is, in practice, the easiest way to hit a meaningfully higher fiber intake, because whole plant ingredients — not the refined, stripped-down versions found in most packaged food — are naturally fiber-rich. A homemade lentil soup, a stir-fry loaded with vegetables, a whole grain and bean salad — these effortlessly outpace anything from a packet.

A simple starting goal: add one extra fiber source to each meal — a handful of beans in your rice, a side of vegetables, whole fruit instead of juice.

Herbs and spices that support your gut

Herbs and spices are one of the most overlooked gut-health tools in the kitchen — and one of the easiest to add, since cooking from scratch is what actually makes room for them (pre-packaged food rarely lets you control this).

Some of my go-to gut-supportive additions:

• Ginger — supports digestion and has a long-standing role in easing bloating and nausea
• Turmeric — its active compound, curcumin, has been studied for anti-inflammatory effects relevant to gut health, especially when paired with black pepper for absorption
• Fennel seeds — traditionally used to ease bloating and gas
• Cumin and coriander — support digestive enzyme activity
• Garlic — a prebiotic fiber source that feeds beneficial bacteria
• Cinnamon — has been studied for its effects on blood sugar regulation, which is closely tied to gut and metabolic health

Beyond their individual benefits, herbs and spices add polyphenols — plant compounds that your gut bacteria also ferment and benefit from. Building a well-stocked spice box isn’t just about flavour; it’s one of the simplest upgrades you can make to a dish’s gut-health value.

The 30 plants a week goal

If you take away one number from this post, make it this: aim for 30 different plant foods a week.

This comes from research (including the well-known American Gut Project) showing that people who ate 30 or more different plant types per week had significantly more diverse gut microbiomes than those eating 10 or fewer — and diversity is one of the strongest markers we have of a resilient, healthy gut. However, a caveat here: the plants have to be the real stuff, and cannot be processed foods claiming to contain 5 different plants in a powder or paste form!

The number is less intimidating than it sounds, and it counts more than you’d think:

• Vegetables and fruits (each type counts separately — tomato, spinach, and banana are three, not one “vegetable/fruit” category)
• Whole grains (rice, oats, quinoa, whole wheat)
• Legumes (lentils, chickpeas, kidney beans)
• Nuts and seeds
• Herbs and spices — yes, these count too, and they’re an easy way to boost your number

A bowl of mixed grain salad with three vegetables, a scoop of chickpeas, a scattering of seeds, and a herb garnish can easily rack up 8–10 plants in a single meal. This is exactly where cooking from scratch has the advantage over pre-made meals — a packaged dish typically repeats the same 4–5 base ingredients across every product on the shelf, while home cooking lets you rotate and layer freely.

Check out my post on the 30-plants-a-week challenge for more and download the free planner to get you started!

Try this: keep a running list on your fridge of every plant food you eat this week and see how close you get to 30. Most people are surprised by how low their starting number is — and how quickly small additions move it.

Getting started without overwhelm

You don’t need to overhaul your kitchen or your family’s diet overnight — in fact, I’d actively discourage it. Sustainable gut-health habits are built gradually.

A few starting points I give clients:

• Swap one processed staple for a homemade version each week (start with the one you rely on most)- maybe ketchup, mayonnaise, or mustard? The taste of homemade condiments is much better than store-bought, which need added chemicals and preservatives to make them shelf-stable and profitable. Homemade condiments stay well in the refrigerator for a week or two.
• Add one extra vegetable, legume, or herb to a meal you already cook regularly. A vegetable pilaf instead of plain rice, a generous dash of herbs to your eggs or legumes in your salad.
• Keep your plant-food tally for a week just to see your starting point — no pressure to hit 30 immediately, but trust me, it won’t be a struggle once you get started.
• Batch-cook a base (grains, beans, or a stock) once a week so “from scratch” doesn’t mean starting from zero every night. Meal prep on the weekends, so you can quickly rustle up the weekday meals.
• Make your refrigerator your best friend. Food that is cooked and appropriately refrigerated or frozen retains its nutrient value and, in some cases, even improves it (resistant starch formation in cooked rice).
• Check out the Food/Nutrition section for kitchen hacks, easy weeknight recipes made from wholesome foods, and strategies to get real food on the table without the overwhelm.

Cooking from scratch isn’t about perfection or turning every meal into a production. It’s about giving your gut microbiome the raw materials it actually needs — consistently, and in a way that fits into a real, busy life with kids and a career, not a wellness influencer’s schedule.

Keep following along for more evidence-backed, practical ways to build gut health into your everyday life — starting, always, with what’s on the plate.