Should Lilies Always Be Cut Down in the Fall?

Lilies are relatively low-maintenance plants, and they’re great to have in any yard or garden because of their strong scent and colorful appearance. However, one thing you have to keep up with is the annual cutting down and trimming of the plant. Luckily, only minimal pruning is required.  

Lilies should always be cut down in the late fall because cutting down dead blooms and stems helps the plant focus its growing energies on new bulbs and future growth. Additionally, cutting down lilies maintains a controlled and pleasant appearance. 

In the rest of this article, I’ll explain why it is important to always cut down lilies in the fall. I’ll also describe some common diseases and pests lilies are susceptible to so you can look for symptoms while you prune. If you want to keep your lily plants looking and feeling good for many growing seasons, keep reading! 

How to Properly Cut Down Lilies in the Fall

In addition to ensuring that the plant focuses its energy and resources on new growth, cutting down lilies also helps the appearance of the plant. You need to groom your lilies every fall, but only a minimal amount of pruning is needed to keep the plant healthy and looking good.

Let’s take a look at the steps for pruning your lilies.

First, you should always use clean, disinfected, high-quality pruning shears with sharp blades to cut down your lilies.

After getting your shears, the next step is removing the blooms as soon as they start to fade. Lilies only bloom once per season, so removing the dead bloom doesn’t hurt your chances of seeing another pop of color later in the same season. 

It is important to remove the blooms once they begin to fade because if they are left in place, they will produce seeds, and this uses up energy that the plant could be using to prepare for future growth. To remove these flowers, you can cut them to display in a vase, or you can pinch off the flowers. 

Cutting lilies for use in floral arrangements is simple. Try to leave as much of the stem as possible to help next year’s growth. You should cut the flowers in the early morning when the flowers are most hydrated, and be sure to have a bucket of water with you to submerge the stems as soon as you cut them. 

When the growing season ends, the foliage will begin to yellow and fade. Wait until the foliage is completely dead before you cut it down because the foliage is still providing nourishment for the next season. This usually happens in late fall. When it’s time, cut the stalk at the base.

Cutting down your lilies helps you control where the plant’s energy is going and how the plant grows. It is one of the best ways to maintain a healthy lily plant for many growing seasons, and cutting down dead or unsightly foliage helps you maintain the look you want for your garden. 

Lily Diseases and Pests  

Another reason pruning is beneficial is because it allows you to check for signs of disease and pests. Lilies are relatively disease-resistant, but they are susceptible to mosaic virus and root rot.

The following table outlines the symptoms of these diseases, so you know what to look out for while you’re cutting your plant: 

Mosaic Virus
  • Yellow or white spots on foliage
  • Disfigured leaves
  • Yellowing of veins
  • Stunted growth
  • Dry stems
Root Rot  
  • Stunted growth
  • Premature yellowing of foliage
  • Rotten portions on roots and bulbs

If you notice these symptoms, the best thing to do is cut off any disfigured or discolored leaves and stems. These diseases can reach a point where it is necessary to dig up the entire plant, which should be done quickly to avoid spreading the disease to other plants in your yard. 

In addition to keeping an eye out for disease as you cut your lilies down, you should also look for pests. Lilies are prone to attack by many kinds of pests depending on where you live.

Here are some common culprits:   


Aphids, or plant lice, are a group of insects, including over 4,000 species of parasites that spread viruses and cause distorted leaves, flower buds, and stems. They feed on phloem sap, which causes a metabolic imbalance that can lead to leaf loss. 

Lily Leaf Beetles 

Lily leaf beetles have been reported in Europe, eastern and northern United States, and eastern Canada. These beetles feed on the leaves of lilies and seem to have bottomless appetites, as they can eat an entire plant in just two hours. The adults and the larvae chew irregular holes in leaves, stems, and buds.

The beetles are bright red and a quarter of an inch long. They have dark-colored legs and undersides, making them difficult to spot if they are upside down and playing dead, which they often do when disturbed. 

The larvae are slug-like, squishy, and yellow in color with black heads. The eggs are less than a tenth of an inch long and reddish. The eggs are usually laid on the underside of leaves in groups of a dozen. 

If you don’t have many lilies, you can hand-pick and crush the beetles and their eggs. You can also use an insecticide that contains neem. Neem is effective in killing larvae and helps control the disease.   

Lily Thrips 

Thrips are tiny, winged insects that can be yellow, brown, or black in color. They suck plant cells from lilies, which causes streaks and white patches on foliage and stunted flower growth. The larvae like to live in the bulb of lilies, which weakens it and allows bacteria and fungi entry. They can also easily spread viruses. 

You can remove thrips by shaking the plant and catching them on a piece of cloth underneath the plant. You can also treat the bulbs with a hot water treatment and then dust them with benzene hexachloride


Nematodes are microscopic multicellular animals that are worm-like in appearance and can inhabit soils in all regions. The most harmful kinds of nematodes to lilies are the root lesion, meadow, and leaf-lesion species.

These creatures penetrate the roots and lay eggs, killing the plant cells. Eventually, the roots succumb to infection and become useless piles of mush.  

To eliminate nematodes, you can use an insecticide and fumigate the soil with methyl bromide and chloropicrin. You should also treat the bulbs with a hot water treatment. 

Cutting down your lilies is a great opportunity to eliminate any diseased or pest-infected flowers and stems. The activity also encourages you to pay closer attention to your plant to look for potential symptoms. 


After your lilies are done blooming, and the leaves are completely brown, which is typically in the late fall, it is best to cut them down. This helps the plant distribute its energy and resources to new growth instead of dying blooms. Cutting down in the fall also helps you check for signs of disease or pests. If you plan on keeping your lily plant for more than one season and want to see bright and beautiful flowers, you should cut down your lilies in the fall. 

Alexander Picot

Alexander Picot is the founder of and its lead content writer. He created the website in 2022 as a resource for horticulture lovers and beginners alike, compiling all the gardening tips he discovered over the years. Alex has a passion for caring for plants, turning backyards into feel-good places, and sharing his knowledge with the rest of the world.

Recent Posts