Straining tomato seeds is straightforward once you pick the right method for your goal. Whether you’re making a smooth sauce, preparing tomatoes for canning, or saving seeds to plant next year, the approach differs slightly. Here’s how to handle each situation.
Why Bother Removing Tomato Seeds
Tomato seeds contain tannins that can add bitterness to sauces, especially when simmered for a long time. Removing them before cooking gives you a smoother, milder result. Seeds also create a texture some people find unpleasant in purees, soups, and pasta sauces. That said, the seeds themselves are nutritionally dense: about 25% protein, 20% fat, and 35% dietary fiber by weight. So if texture and bitterness aren’t a concern for your recipe, leaving them in is perfectly fine.
One common reason people strain seeds is a belief that they aggravate diverticulitis. Research published in the Annals of Internal Medicine found no association between eating seeds (including those in raw tomatoes) and developing diverticulitis. Women who ate the most nuts, seeds, and seed-containing fruits had essentially the same risk as those who ate the least. So if that’s your only reason for straining, you can skip it.
The Cut-and-Squeeze Method
For small batches or when you want raw, uncooked tomato flesh, this is the simplest approach. Cut the tomato in half horizontally (across the equator, not stem to bottom). This exposes all the seed cavities at once. Hold each half cut-side down over a bowl and gently squeeze. The seeds and surrounding gel slide right out. You can use your finger or a small spoon to scoop out any stragglers from the cavities.
This works best for recipes where you want chunks of tomato without seeds, like bruschetta, fresh salsa, or salads. It won’t give you a puree, but it’s fast and requires no special equipment.
Using a Fine-Mesh Sieve
If you’ve already chopped or crushed your tomatoes and need to separate seeds from juice or pulp, a fine-mesh sieve does the job. Set the sieve over a bowl, pour in the tomato mixture, and press it through with the back of a spoon or a rubber spatula. The pulp and juice pass through while the seeds stay behind. Work in small batches so the sieve doesn’t get clogged.
Periodically scrape the underside of the sieve to keep liquid flowing freely. This method is ideal for extracting fresh tomato juice or for straining a quick uncooked sauce.
The Food Mill Approach
A food mill is the traditional tool for making tomato sauce, and it’s the most efficient way to strain seeds from cooked tomatoes. It’s a hand-cranked device with a rotating blade that pushes soft food through a perforated disc at the bottom. The disc lets pulp through while trapping seeds and skins.
To use one, cook your tomatoes until they’re soft (roughly chopped is fine, no need to peel or seed beforehand). Set the food mill over a large bowl or pot, add a few ladlefuls of cooked tomato, and crank the handle clockwise. Every so often, reverse direction to scrape seeds and skin off the disc so it doesn’t clog. Keep cranking until the material left behind is dry and spent, then discard it and add more tomato.
For seed removal, choose a disc with 1.5 mm (1/16 inch) holes, which blocks all tomato seeds. A 2 mm (3/32 inch) disc works too and processes slightly faster, though a few smaller seeds may sneak through. Most food mills come with two or three disc options.
Blanching First Makes Everything Easier
If you plan to strain a large batch, blanching loosens the skins and softens the flesh so the tomato breaks apart more easily. Score a shallow X on the bottom of each tomato with a knife. Drop them into boiling water: 30 to 45 seconds for small tomatoes, 60 to 90 seconds for large ones. Cherry tomatoes need only 20 to 30 seconds, while big beefsteaks can take up to 2 minutes. Watch for the skin at the X mark to start curling away from the flesh.
Transfer the tomatoes immediately to a bowl of ice water and let them sit for 2 to 3 minutes. The skins will peel off with almost no effort. From there, you can halve and squeeze out seeds by hand, or crush the tomatoes and run them through a sieve or food mill. Blanch tomatoes of similar sizes together so they cook evenly.
Electric Strainers for Large Batches
If you’re processing bushels of tomatoes for canning, an electric tomato strainer saves hours. These machines use a motorized auger to push cooked tomato through a screen, separating pulp from seeds and skins automatically. Commercial-grade models can handle 200 to 350 pounds per hour. You feed quartered, lightly cooked tomatoes into the hopper, and finished sauce comes out one side while seeds and skins exit the other.
For most home cooks doing a few dozen jars a season, a hand-cranked food mill is more practical and far less expensive. Electric strainers make sense when you’re regularly processing 50 pounds or more at a time.
Straining Seeds for Saving and Planting
If your goal is to collect tomato seeds for next year’s garden, straining works differently. You actually want to keep the seeds, not discard them, and the gel coating around each seed needs to be removed first. That gel contains germination inhibitors, so seeds planted with the coating intact won’t sprout reliably.
Squeeze tomato pulp, seeds, and juice into a jar or cup. Add a splash of water, then leave the mixture at room temperature for 24 to 96 hours. A layer of mold will likely form on top during this time, which is normal and actually helps break down the gel. Stir the mixture once or twice a day. When fermentation is complete, the viable seeds will have sunk to the bottom.
Pour off the mold, liquid, and floating debris. Add fresh water, swirl, and pour off anything that floats. Repeat until the seeds at the bottom are clean. Then strain them through a fine-mesh sieve, rinse under running water, and spread them on a plate or paper towel to dry completely. Store dried seeds in an envelope or small jar in a cool, dry place. They’ll stay viable for several years.