The Best Natural Puppy Food: A Holistic Feeding Guide

Getting a puppy has to be one of life’s greatest pleasures.

It’s not all sunshine and roses…puppies are like babies with sharp teeth! 🦈

You’re excited (if not a little nervous) about it all. Puppy-proofing, teaching obedience, potty training, and figuring out what to feed your pup are all part of the deal.

If you’ve ever stood in front of a wall of puppy food wondering where to even start, you’re not alone. 

Every bag claims to be the best, every label looks healthy, and every online article seems to say something different. 

Ask a traditional veterinarian, a holistic veterinarian, and a veterinary nutritionist, and you might get three different answers.

It’s confusing, and it shouldn’t be.

When people come into the store and ask what to feed their puppy, I can tell they want the same thing I do: a healthy, happy dog who thrives from the inside out. 

I've done the research for you over the last 30+ years, based on science, and have broken down my findings for you here.

Once you understand what your puppy’s body truly needs and how to recognize real, nourishing ingredients, the choices become much clearer.

In this guide, we’ll look at what makes a diet “natural” from a biological point of view, compare raw and kibble feeding, and unpack the grain-free debate so you can choose puppy food with a more discerning eye.

What Puppies Really Need For a Healthy Start

When you think about the best natural puppy food for your little one, remember one simple thing: they’re growing every single day. 

Their bones are stretching, muscles are forming, organs are developing, and their brains are busy wiring new connections. All that growth takes fuel…but not just any fuel.

Puppies need real food that delivers energy, protein, healthy fats, and all the vitamins and minerals that support their development. 

Here’s what that means in everyday terms:

Protein: This is the foundation. Puppies need high-quality animal protein to build strong muscles, a healthy immune system, and a shiny coat. 

The better and more varied the protein source, the more your puppy’s body can actually use it.

Fat: Healthy fats give puppies concentrated energy for all that growing and playing. They also support skin, coat, and brain development. 

Look for foods that contain natural sources of omega-3 and omega-6 fatty acids from animal-based, plant-based, and marine-based fats.

Calcium and minerals: These are the building blocks for bones and teeth. Puppies need the right balance of calcium and phosphorus. Too little or too much can cause problems later. 

This is especially important for large-breed puppies, whose bones grow quickly.

Vitamins and trace nutrients: Think of these as the spark plugs for your puppy’s body. They keep digestion, immunity, and metabolism running smoothly. 

The best natural puppy foods include them, but they can also come naturally from fresh meats, eggs, fruits, and vegetables.

Water and moisture: Don’t overlook hydration. Puppies on dry food need more water than those eating fresh or lightly cooked food. 

Proper hydration keeps digestion moving and helps every organ function properly.

Certified veterinary nutritionists often say that any diet, whether raw pr cookedshould check three boxes: it must be 

• complete, 

• balanced, and 

• digestible. 

That’s what sets a strong foundation for lifelong health.

Raw vs Kibble for Puppies

This is the question that usually sparks the longest conversations in the store. 

Some people are drawn to raw feeding because it feels natural and unprocessed. 

Others prefer the convenience and consistency of dry food. 

The truth is, both have their pros and cons, and the best choice often depends on your comfort level, your puppy’s health, and how much time you can commit to feeding and handling food safely.

Kibble might be the most familiar option, but it’s also the most processed. 

The high heat used in manufacturing damages delicate nutrients and enzymes. 

How do manufacturers combat this problem? They add synthetic vitamins added back in to meet nutritional standards. Not ideal.

Even when it looks “healthy” on the label, kibble is still a product of intense processing. 

>>And don’t be fooled by labels that proclaim “veterinarian approved.” Many veterinary schools receive nutrition education support or materials from large commercial pet food companies, so many traditional vets are trained within that framework. 

It’s not that their advice is wrong, but it often reflects the products and philosophies of those sponsors rather than a broader, whole-food perspective.

For people who want something dry and convenient but closer to real food, freeze-dried or air-dried diets are a much better choice. They preserve more nutrients and natural flavor while offering the same easy storage and scoop-and-serve simplicity.

Raw food appeals to many holistic pet owners because it more closely resembles what dogs are built to eat. 

Raw diets are higher in moisture and rich in enzymes that can support digestion and skin health. 

But raw feeding isn’t as simple as tossing your puppy some meat. It needs to be nutritionally balanced and handled with care. 

Puppies are still developing their immune systems, so food safety is especially important. 

If you’re feeding raw, look for balanced commercial options that meet AAFCO growth standards or work with a holistic vet or certified veterinary nutritionist who can help you build a complete plan.

Many people find that a hybrid approach works best. Feeding a combination of gently cooked, freeze-dried, or raw foods alongside high-quality, limited-ingredient kibble can give your puppy the best of both worlds. 

What matters most is that the food is fresh, species-appropriate, and balanced for growth.

If you’re not sure where to start, our Healthy Animal Healing Center staff can help you choose safe, natural options and walk you through how to transition your puppy gradually. 

The goal isn’t perfection; it’s building a diet that supports your puppy’s long-term health and fits comfortably into your life.

By the end, you’ll have a grounded understanding of what “healthy” really means for your puppy and the confidence to make feeding choices that align with your values and your dog’s needs.

Whatever option you choose, it’s worth checking who actually formulated it. 

Some of the best natural puppy food brands work with board-certified veterinary nutritionists, professionals who specialize in balancing diets for safety and long-term health. 

Their oversight helps ensure the right mix of protein, fat, calcium, and other nutrients your puppy needs to grow strong. 

If a company is transparent about who designs their recipes, that’s a good sign. It means they care as much about what’s in the food as how it’s marketed. 

Spoiler alert: We check for this before we ever put anything on our shelves.

Grain-Free vs Whole-Grain Puppy Food

Few topics create more confusion than whether dogs should eat grains. 

Some people swear by grain-free diets, while others are certain that avoiding grains can cause heart problems. The truth, as usual, lives somewhere in the middle.

Let’s start with where this debate came from. A few years ago, the FDA began investigating a possible link between grain-free dog foods and a heart condition called dilated cardiomyopathy (DCM). 

The concern centered on certain boutique diets that replaced grains with peas, lentils, or other legumes. Some dogs eating these foods developed heart issues, but studies since then haven’t proven that the absence of grains was the cause. 

The problem seems to have more to do with the overall formulation and nutrient balance than with the lack of grains.

Holistic veterinarians like Dr. Judy Morgan have spoken out about how the early grain-free panic may have been overblown. She points out that many of the diets in question had other red flags, including unusual ingredients or unbalanced nutrition, and that blaming the grain-free label alone oversimplifies a much bigger issue.

Dr. Karen Becker offers a complementary view. She encourages pet parents to focus less on whether a food contains grains and more on how processed the food is. 

Her advice is to choose diets made from whole, fresh, minimally processed ingredients and to steer clear of highly refined grains and fillers. In her view, quality matters far more than whether a diet includes or excludes grains.

So what does that mean for your puppy? 

It means you don’t need to fear grains, and you don’t need to chase grain-free labels either. 

What matters is the source and purpose of those ingredients. The best approach is to look at the entire recipe, not just one ingredient trend. 

Choose foods that start with high-quality animal protein, avoid unnecessary starches, and, if you want to include grains, keep them whole and minimal.

If you’re unsure which route is right for your puppy, we can help you sort through the options and find a diet that fits your dog’s individual needs and your comfort level.

Finding the Best Natural Puppy Food for Your Dog

Feeding your puppy doesn’t have to be confusing. 

Once you understand what their growing body truly needs and how to spot quality ingredients, it’s much easier to make good choices. 

Whether you feed raw, lightly cooked, freeze-dried or air-dried food, the goal is the same: real nutrition that supports healthy growth and a long, happy life.

Every puppy is different, and there’s no single recipe that fits them all. 

If you’d like help choosing food that matches your puppy’s breed, size, and lifestyle, stop by The Healthy Animal Healing Center. We can walk you through natural options, explain ingredient labels, and help you find food you can feel good about feeding.

Because feeding your puppy well isn’t about following trends or falling prey to excellent marketing.

It’s about giving them the start that will carry them for a long, healthy life.

Further Reading

If you’d like to explore more about natural nutrition for puppies, here are some of the trusted sources that helped shape this guide:

Holistic Veterinarians

• Dr. Karen Becker, holistic veterinarian and author on species-appropriate nutrition and fresh feeding

• Dr. Judy Morgan, integrative veterinarian known for her work in whole-food diets and balanced homemade feeding

Veterinary Nutrition and Science

• The Merck Veterinary Manual, Nutritional Requirements of Small Animals

• Cornell University College of Veterinary Medicine, Re-Evaluating Your Dog’s Diet

• American College of Veterinary Nutrition (ACVN), Board-Certified Veterinary Nutritionist Directory

• Frontiers in Veterinary Science, Taurine Status and Grain-Free Diets in Dogs: A Review of Current Evidence

• National Research Council, Nutrient Requirements of Dogs and Cats