How to Make Healthy Homemade Pizza From Scratch 

 Last Update November 11, 2022

By Jenny Z

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We are huge pizza lovers here and I want to share with you how to make healthy homemade pizza from scratch!

I love making homemade pizza because it is very easy and fun to make, simple to prepare, and yet hit the spot! Not mentioning it is much healthier and cheaper than going out or ordering in. You can pretty much put whatever you want on your pizza with ingredients you personally picked out, therefore, you know exactly where your food comes from, how it was made and what you are consuming.

Why make your own pizza?

The reason why I prefer homemade pizza, besides it, is healthier and cheaper, it is because homemade simply tastes better! To me, knowing what you are eating and where your food comes from is very important because it is directly linked to your health and well being. And nothing beats using organic and fresh ingredients.

Have you heard of dirty dozen? Dirty dozen is highlighting the fruits and vegetables most likely to harbor pesticide residues. According to Environmental Working Group's 2017 shopper guide to the pesticides in produce, here are the dirty dozen:

  1. Strawberries
  2. Spinach
  3. Nectarines
  4. Apples
  5. Peaches
  6. Pears
  7. Cherries
  8. Grapes
  9. Celery
  10. Tomatoes
  11. Sweet Bell Peppers
  12. Potatoes

Many of these ingredients are commonly used in pizza. Which means unless you know where your local pizzerias source their ingredients and what ingredients they are using, you are probably eating pizza with ingredients contain a high level of pesticides and ingredients you can't pronounce.

Why should you avoid dining in or take out?

Recently, the USDA conducted a study which revealed the enormous amount of pizza we consume in the United States. American consumption of cheese increased by nearly 30% in 10 years because the dairy industry is spending big bucks to promote pizza and partner with big chains like Dominos. But there’s a lot going on behind closed doors and us as consumers are left in the dark. As a result, we don't know what is going in into our pizza and what exactly we are eating.

Vani Hari, the author of Food Babe, conducted an investigation to see what ingredients were in pizza from the popular chain like Domino's, Pizza Hut, Little Caesars, California Pizza Kitchen, and Papa John's. Hari couldn't find any ingredients listed on their website and when she called them up, they all refused to provide her with the information. Even her local pizzeria was not willing to provide her with the information. What she did find from her investigation is that there are lots and lots of hidden MSG! Instead of using actual MSG, which could give the restaurant a bad reputation, restaurants are adding potent flavor enhancer without average consumer realizing it. Instead of letting us know that they are putting in MSG in our food, they are using an FDA loophole to sneak processed glutamic acid into our food, which as the same effect as MSG.

To learn if your food truly contains processed free glutamic acid (MSG), Truth In Labeling has got your back with names of ingredients that contain processed MSG.

When to Eat Pizza?

I'm not saying you have to follow this rule but just something you should think about, pizza should never be eaten at night. The good news is, you can still eat it for lunchtime.

Nutritionists advise that people should avoid eating a heavy meal at dinner time, like pizza. Eating a heavy meal at night creates the perfect environment for disrupted sleep, owing to our stomach’s skilled ability to pump out acid at the first sign of food. Fact is, plenty of us end up eating late at night. But if you’re prone to heartburn, a symptom of acid reflux, chowing down too close to bedtime is the worst thing for you. Considering acid reflux affects an estimated 20 percent of the population, this may be you.

If you do experience acid reflux, three best advise to you:

  • Don’t eat within three hours of going to bed.
  • Set a snacking cut-off time.
  • Make your last meal of the day smaller and lighter.

Ways to make healthier pizza:

  • Replace your white flour with whole-wheat flour, chickpea flour, or veggie crust (cauliflower, zucchini, summer squash, portobello, quinoa).
  • Make your own pizza sauce. If you are purchasing from the store, avoid sauce that is packed with sugar.
  • Replace your traditional pizza sauce with other sauce like hummus, pumpkin puree, garlic paste, salsa, garlic coconut sauce, peanut sauce...
  • Avoid overloading your pizza with cheese! I know, we all love a cheesy pizza.
  • Go green with basil or kale pesto sauce.
  • Dessert pizza, replace your Nutella with a dark chocolate spread.
  • Replace your sausage and pepperoni with grilled chicken, tofu, nuts, eggs or beans.
  • Load your pizza with greens, and even fruits!

How long does rising take?

You will need the dough to rise for at least an hour. The good news is you can speed up or slow down the process.

If you decided to make the pizza at a later time, you can refrigerate the dough to slow down the rising process. It will take about 12-24 hours for fermentation to end.

To speed up the fermentation process, you have few options:

  • You can speed up fermentation with temperature, by allowing your dough or batter to rise in a warmer environment. For example, turn your heater.
  • If you’re feeling like tweaking your recipe, you could speed up fermentation by adding additional ingredients—diastatic malt or a small amount of sugar.
  • Oven rising- The oven temperature should not exceed 90°F during the rising time. Place a pan of very warm water toward the back of the oven to provide moisture, which keeps the dough soft during rising. Place the covered bowl or pan of dough on the center rack and close the door.
  • Microwave rising- Place 1 cup of water in a glass measuring cup in the microwave. Heat on high for 2 minutes. This creates a moist environment to keep the dough soft during rising. Place covered bowl of dough in the microwave and close the door.

How do I know when the dough is ready?

Yeast dough is considered “ripe” when it has risen enough – usually doubling in size. The ripe test determines if the dough is ready to be punched down and shaped.

Gently stick two fingers in the risen dough then take them out.If the indentations remain the dough is “ripe” and ready for punch down. If not, cover and let the dough rise longer. Repeat test.

Pizza stone vs baking pan

Pizza can be baked on baking pans or pizza stone and which one to use is a matter of preference.

With a stone, you have to preheat the stone until completely heated (~30 minutes) while you build a pizza on the counter and transfer the pizza from the counter to the hot stone with a pizza peel. The benefit of using a stone is you can make any shape and size pizza you want, as long as it fits on the stone. As with a pan, the pan determines the size and shape. Compared to the metal of a baking sheet, a pizza stone holds heat more evenly, and the porous surface draws water out of particularly wet areas of the dough as it cooks.

With a pizza pan, you can build the pizza in the pan and place the pan in the oven.  For me, a pan is more convenient. The benefit of the pan is they are easy to clean and store.  Stones are brushed or wiped clean and put away.  If you drop a stone, it will break.

Mix and match your favorite meats, cheeses, and vegetables with:

  • Marinara
  • Alfredo sauce
  • Pesto
  • BBQ sauce
  • Or just sauceless its cool too

Need more topping inspirations?

Bonus and tips:

  • Leftover pizza can turn to other dishes like a casserole, pizza patty melt, pizza croton etc.
  • You can freeze pizza dough in any quantity — just let it fully rise before you freeze it. The dough can be frozen for up to three months and just needs to be thawed in the fridge overnight before you use it!

Homemade Pizza With Quick and Easy Pizza Crust Recipe

Prep Time 20 Minutes
Cook Time 15 Minutes
Passive Time: 30 Minutes

Serving Size 4 People


Pizza Dough: 

3 Cups whole wheat flour
(You can do 2 cups wholewheat and one cup coconut flour for extra protein)
1 1/4 cup Warm water
1 packet
Active dry yeast
2 Tablespoon
Extra virgin olive oil
2 teaspoon
Himalayan Salt
1 Tablespoon
coconut sugar

Topping option 1: Rosemary Chicken And Potato Pizza

Fresh Garlic Organic
Himalayan Salt
Lemon juice Organic
Potato Small or medium
Dried Rosemary
Extra virgin olive oil
BBQ Sauce
Sweet onion Organic
Mozzarella cheese Organic

Topping option 2 : Pesto veggie

Pesto Organic
Mozzarella cheese Organic
Mushroom Organic
Pepper Organic, red, yellow or green
Onion Organic


Traditional Dough

  1. Combine flour, yeast, salt, sugar and olive oil in a bowl.

  2. Slowly add 1 1/2 cup of warm water. Additional water may needed.
  3. Knead until the dough is smooth and firm ball that is not too dry.
  4. Once is done, cover the bowl with a damp kitchen towel or paper towel. Let it rise for at least 30 minutes.
  5. Roll out the dough and poke few times with a fork at random spots to prevent bubbling when baking.

Topping option 1: Rosemary Chicken And Potato Pizza

  1. Slice the potatoes and coat it with garlic, rosemary and olive oil. Coat thoroughly.

  2. Grill or pan the chicken with garlic, salt and olive oil for about 10-15 minutes. Once its cool down, slice the chicken into cubes. Avoid overcooking the chicken because you will cook it again when baking the pizza.
  3. To make the pizza, spread your favorite BBQ sauce, and then a layer of cheese. Top it with cooked chicken, potato, and sliced onion. Once you are done assembling it, bake the pizza at 415F for 12-15 minutes.

Topping option 2: Pesto veggie

  1. Slice pepper, mushroom and onion.

  2. Spread your pesto sauce on top of the dough. Then add cheese and your sliced toppings. Once it is complete, bake it at 415F for 12-15 minutes.

Did you make this recipe?

Tag @organicallyblissful on Instagram or hashtag it #organicallyblissful

Jenny is a health-conscious, organic and natural lifestyle influencer with a Bachelor's degree in science. With years of experience working in food sciences with organic products and health & nutrition companies - she firmly believes that a natural lifestyle is healthier for you and better for the environment as well.

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