9 Annuals You Need to Remove in Fall (and Why It’s Essential)

As fall rolls in and the air turns crisp, it’s tempting to let your garden wind down on its own. But if you want a healthy, thriving garden next year, there’s one key task you can’t skip: removing your annuals.

I’ve learned the hard way that leaving dying plants in the ground can invite pests, diseases, and a big mess for next spring. Plus, it frees up space for new plants and helps the garden breathe again.

Let’s talk about nine annuals you should remove before winter sets in, and why it’s so important.

Marigolds
Marigolds

Marigolds are such a delight in the garden, especially because they repel pests like a charm. But once the season is over, leaving them in place can backfire. I found out the hard way when a patch of marigolds I left behind turned into a fungus farm.

After they die, marigolds can invite fungal diseases, especially in cool, damp conditions.

How to Remove: Uproot the plants and compost the healthy ones. If they look diseased or moldy, toss them in the trash.

Petunias
Petunias

Petunias are gorgeous all summer, but by fall, they often become straggly and weak.

I used to leave them in the garden, thinking they’d survive the first frost. Spoiler alert: they didn’t, and they brought pests with them!

Petunias get leggy and prone to mold, which can lead to pest problems if left too long.

How to Remove: Pull up the plants gently. Compost the healthy bits, but toss anything moldy in the trash.

Zinnias
Zinnias

Zinnias are one of my favorites for their bold colors, but they’re also prone to powdery mildew late in the season. I once made the mistake of leaving them too long, and the mildew spread to my other plants.

How to Remove: Cut the plants at the base and compost them only if they’re disease-free. If you see any mildew, throw them away.

Hardy Geranium
Geranium

Annual geraniums are beautiful through summer, but they don’t do well when temperatures drop. I’ve left them in the garden before, only to find a soggy, rotting mess when spring rolled around.

When the weather cools, geraniums can start to rot if left in wet soil.

How to Remove: Pull them up, compost healthy plants, or bring them indoors if you plan to overwinter them.

Begonias
Begonias

I love begonias, but I’ve learned not to leave them in the ground once fall arrives. They’re quick to rot when the temperatures drop, and they don’t look pretty by that point anyway.

Begonias, especially the tuberous types, die back quickly and can rot in cool, wet conditions.

How to Remove: Dig them up, save the tubers if you want to reuse them next season, or discard the entire plant if not.

Impatiens
Impatiens

Impatiens are garden showstoppers, but they’re incredibly susceptible to downy mildew. One year, I ignored the signs of mildew, and it spread faster than I could control. Now, I always remove them before it’s too late.

How to Remove: Uproot the entire plant and dispose of it. Don’t compost mildew-infected plants.

Sunflowers
Sunflowers

Sunflowers are stunning while they’re blooming, but after they’ve had their moment, they can attract unwanted pests. I left a patch standing one fall, and by winter, aphids had made themselves right at home.

How to Remove: Cut down the stalks, remove the root system, and clear all debris to prevent pests from lingering.

Nasturtiums
Nasturtiums

Nasturtiums are wonderful for attracting beneficial insects, but once they start to die back, they can attract pests like aphids that can overwinter in the soil.

I’ve learned to pull them up before they create problems.

How to RemovePull up the plant and its roots. Healthy plants can be composted, but discard pest-infested plants.

Cosmos
Cosmos

Cosmos are easy to grow, but by the end of the season, they can leave behind a mess of rotting stems and scattered seeds.

One year, I let them go wild, and I ended up with cosmos popping up in all the wrong places the next spring!

How to Remove: Pull them up from the base and clear any scattered seeds to avoid surprise growth next season.

Clearing out your annuals in the fall may not be the most glamorous gardening job, but it’s essential for a healthy, pest-free garden next year.

By removing these nine annuals—marigolds, petunias, zinnias, and more—you’ll be preventing diseases, pests, and unwanted growth, all while making space for next season’s plants.

Trust me, a little cleanup now will make all the difference come spring. So grab your gloves, get outside, and give your garden the fall TLC it deserves!

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