How to Prune Aerogarden Tomatoes

Throughout the pandemic, I grew delicious, fresh tomatoes in my garage using an Aerogarden Harvest garden. When going out to the supermarket was nearly impossible — and so many things were out of stock — it was wonderful to pick tomatoes at home, even in the middle of winter.

Aerogardens make growing food at home (in limited quantities, at least) very easy. But if you’re planning to grow tomatoes in your Aerogarden, it’s essential to prune them properly. The right steps aren’t always obvious from the documentation which comes with the tomato seed pods or the Aerogarden itself.

Here’s what you need to know to prune your tomatoes properly. The good news? Do it right, and Aerogarden says you can keep your tomatoes growing for over a year, harvesting fruit continuously.

Space Your Plants Properly

Many Aerogarden models have six holes, into which you insert seed pods. A tomato seed pod kit comes with six pods. So, when you go to plant tomatoes in your Aerogarden, how many pods should you insert?

If you said “six”, that seems totally logical. But unfortunately, it’s not correct.

While a six-pod Aerogarden can grow six pods of basil, dill or other smaller plants, it can only accommodate about two tomato pods. Aerogarden tomatoes grow big, and they grow fast. It seems counterintuitive, but you’ll actually get more tomatoes with fewer plants in the unit. Otherwise the plants crowd each other out for access to the grow lights, and no one wins.

When starting your garden, plant two pods at opposite ends of the garden. Make sure to cover the open holes with dedicated hole covers, covers you 3D print at home, or gaffer’s tape. Otherwise, light hits the water inside and algae can grow.

Did you miss this step, and already plant more than two plants? I’ve been there. The best bet is to yank a few out, cut off their plastic pods, and transplant them into a real pot outside.

Do a First Pruning at 4–5 Weeks

At 4–5 weeks, your plants should be about one inch tall. Now comes the hard part — it’s time to remove several of your growing plants, so that the healthiest ones remain and yield fruit.

Nature is unpredictable. To ensure that your Aerogarden grows plants, the company loads each seed pod with too many seeds, to make sure that at least one germinates. At 4–5 weeks, it’s likely that you’ll have 2–3 plants growing out of each pod. That’s too many to grow comfortably, so it’s essential to remove extra plants so that each pod has only one plant growing from it.

Examine each pod, and select the tallest and strongest-looking plant. Snip back any other plants growing from the pod near their base, so that only the strongest plant remains. It feels wrong, but it’s essential to ensure that the plants don’t crowd each other out down the line.

To do the actuals snipping, Aerogarden makes a pair of dedicated pruning sheers that’s the right size for delicate plants. It has stainless steel blades, so it cuts cleanly and minimizes damage to your tomatoes’ stems.

Top Your Plants at 6 Weeks

At six weeks, your plants will be starting to get pretty big. Now, it’s time to “top” them by removing some of the stems from the very top of each one. This process helps to keep the plants contained, and to focus their energy on yielding fruit down the line, instead of growing tons of green matter.

According to SF Gate, the topping process goes like this:

Place [your fingers] at the base of the main stem and follow the stem upward until you come to a cluster of leaves and flowers and where the main stem branches out into a “Y.” Cut just below the “Y.” This helps to strengthen the stem to carry the weight of the tomatoes.

Again, it might be hard to cut off the tops of your developing plants. I thought about it like giving them a haircut. Yes, you’re removing some stem. But you’re setting the plants up for solid growth down the line.

Prune Mature Plants Every 2 Weeks

At about 5–7 weeks, your plants will start to flower, and at 9–12 weeks, you’ll have fruit! Remember to raise your grow lights a bit at a time to ensure proper spacing from the tops of your plants. Once your plants are mature, prune them every two weeks to keep them contained.

Aerogarden says to “prune the new growth” off the top of the plant, ensuring that you remove the tips of each stem. “After the plant determines that growing upward is not an option, it will send out new branches lower down on the stem”, the company says. This means it will yield more fruit, and hopefully avoid bumping into the grow lights.

If your plant is already growing into or beyond the lights, it’s time to get aggressive. Prune the stems back until there’s a few inches of clearance below the lights.

This might mean cutting off some blossoms or even growing fruit, but it’s essential to keep your plants growing well. Ideally, though, if you’ve pruned properly all along, your plants will never reach this point.

With proper pruning, you can keep your plants growing for a year or more. My own tomato plants yielded fruit for about 8 months. Pruning is a simple process (again, think “plant haircut”), and ensures a healthy, high-yielding tomato plant in your Aerogarden.

My Recommendations

  • Looking for a new Aerogarden? I’ve been testing the Harvest Elite, and it works great. The growth counter on the garden — which shows how many days it’s been since you planted your pods — is really helpful for knowing when to begin pruning.
  • I grew tomatoes for over a year using these tomato pods.
  • Aerogarden makes a dedicated pair of pruning sheers that are great for pruning your tomatoes.

This article contains affiliate links that support my writing. As an Amazon Associate I earn from qualifying purchases.

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