Can I Delete A Website In Hostinger That Is Opnly In The Domains Folder

Yes, you can delete a website in Hostinger that exists only in the domains folder. But here is the catch: what you delete and how you do it determines whether the domain registration, email accounts, or other services stay or go. This article explains exactly what happens when you remove files from the domains folder, what happens if you delete the website from the Hostinger dashboard instead, and how to avoid accidentally losing something you meant to keep.

If you have a leftover domain folder with no live site and you want to clean it up, you have two main options. Deleting just the files inside that folder removes the website content. Deleting the entire folder through the file manager is also safe as long as you do not remove the domain registration separately.

The domain name itself is not stored in that folder. It is registered at the account level and appears under “Domains” in your hPanel. Understanding that distinction is the entire answer, so let me break it down piece by piece.

What “Only in the Domains Folder” Actually Means

When you add a domain to a Hostinger hosting account, the system creates a directory tree inside your account’s file system. The path looks like this:

/home/yourusername/domains/yourdomain.com/public_html

The public_html folder is where your website files live. If you never uploaded anything, that folder might be empty or contain only default placeholder files. The parent folder (yourdomain.com) exists as a container for the domain’s files, logs, backups, and sometimes a private_html folder for SSL.

So when someone says “my website is only in the domains folder,” they usually mean the site files exist under that path but the domain itself is still registered and pointed to the hosting account. The domain is not “in” that folder. It is configured at the server level through the hosting panel.

This distinction is critical. Deleting the files inside public_html or even the entire yourdomain.com folder does not touch the domain’s DNS settings, the registration record, or the billing cycle for the domain name.

Where You See the Website in the hPanel

Hostinger’s hPanel has two main areas where this domain appears:

• Websites, This dashboard lists every website you have set up under your account. Each entry shows the domain name and gives you quick actions like Manage, Settings, or Remove. Removing a website here does more than delete files. It can also remove the domain from the hosting account and stop the hosting configuration for that domain.

• Domains, This section shows all registered domain names (whether bought through Hostinger or transferred in). You can manage DNS, renewals, and WHOIS from here. Deleting a domain registration is a separate action from deleting website files.

• File Manager, This is where you see the actual folders. The domains folder is visible here, and you can delete individual files or entire folders.

If your site is “only in the domains folder,” it likely means the website entry in the Websites dashboard may not exist (or you never created one), but the domain folder exists because you either added the domain to the hosting account or a previous website setup left the folder behind.

How to Delete the Website the Right Way

The safest method depends on what you want to keep.

Option 1: Delete Only the Files (Keep the Domain Registration and Hosting Configuration)

Use the File Manager or an FTP client to go into the public_html folder inside your domain’s directory. Select all files and delete them. This empties the site.

The domain folder remains, and the domain will still be pointed to your hosting account. If you visit the domain, you will see a blank page or a default Hostinger holding page (depending on your setup).

This is the best choice if you plan to build a new site later on the same domain. You do not need to set up the domain again.

Steps in File Manager:

1. Log into hPanel and open File Manager.
2. Navigate to domains > yourdomain.com > public_html.
3. Select all files (Ctrl+A or the Select All button).
4. Click Delete and confirm.

That is it. The domain stays active, email accounts linked to that domain remain untouched, and you can re-upload content at any time.

Option 2: Delete the Entire Domain Folder from the File Manager

Some users want to remove the folder completely to clean up the file structure. You can do this using the File Manager or FTP as well.

Steps:

1. In File Manager, go to domains/.
2. Right-click the folder named yourdomain.com.
3. Select Delete.

This removes the folder and all its contents, including any subfolders for logs or private files. The domain registration and DNS settings remain, but the server will no longer have a document root for that domain. When someone visits the domain, they will see a “Website not found” or default server error page because the hosting account no longer has the necessary directory.

If you later want to put a site back, you will need to add the domain again through the Websites dashboard, which re-creates the folder structure.

Option 3: Remove the Website from the Websites Dashboard

This is the most thorough cleaning option within the hosting account. When you remove a website from the Websites dashboard (not just the folder), Hostinger disassociates the domain from the hosting plan. The domain still exists in your Domains list, but it is no longer “attached” to any hosting.

You would see it listed under “Not assigned” or “Unlinked” in some views.

Steps:

1. In hPanel, go to Websites.
2. Find the domain you want to delete and click the three-dot menu (or the Manage button depending on your view).
3. Look for an option like “Remove Website” or “Delete Website.” This is usually at the bottom of the settings page.
4. Confirm the removal.

Hostinger will ask if you want to delete the website files as well. If you check that box, the folder is also removed. If you uncheck it, the files stay in the domains folder but the domain is no longer linked to a hosted website.

This option is the one that most people mean when they ask “Can I delete a website in Hostinger?” but the user here specifically asked about a site “only in the domains folder”, meaning the website entry may already be gone, or it was never created. In that case, only Option 1 or 2 apply.

Important Caveat: What Deleting the Folder Does NOT Do

Note: Deleting the website folder (either the files or the entire directory) does not cancel the domain registration and does not stop domain renewal charges. If you bought the domain through Hostinger, you must go to the Domains section and select “Cancel” or “Don’t Renew” to stop paying for it. The folder deletion only affects the hosted content.

Similarly, email accounts created under the domain (e.g., you@yourdomain.com) remain active even after the folder is gone because email storage is in a separate directory (usually /home/yourusername/emails/ or handled by a separate mail server). If you want to remove those email accounts, you need to delete them individually from the Email section of hPanel.

Common Mix-Ups and Things People Get Wrong

Mix-Up: Deleting the Domain Folder Cancels the Domain Registration

Reality: The domain registration is a contract with a registrar (Hostinger or another company). The folder in your hosting account is just a storage location for the website files. They are completely separate.

You can delete the folder today and the domain will still resolve and show a blank page or error. The domain will also continue to renew on its billing cycle unless you manually cancel it.

Mix-Up: Removing the Website from the Dashboard Removes the Domain from Your Account

Reality: It removes the link between the domain and the hosting plan. The domain itself stays in your account under Domains. You can reattach it to the same hosting plan later, or point it to a different host.

The domain registration stays active unless you also delete it from the Domains section.

Mix-Up: If the Folder Is Empty, Deleting It Does Nothing

Reality: An empty folder still takes up a tiny amount of disk space and can clutter the file manager. Deleting it also removes the default document root, which may cause the domain to show an error instead of a blank page. That might be what you want, but it is not “nothing.”

Mix-Up: Deleting the Website Files Will Stop Email

Reality: Email delivery for your domain depends on MX records, not on the presence of a public_html folder. Deleting the website files does not affect email at all. You can have a working email account on a domain that has no website.

The two services are separate in Hostinger’s infrastructure.

What This Means for You

If you are reading this because you have a domain folder sitting in your Hostinger account that you no longer need, the practical takeaway is straightforward.

First, decide whether you want to keep the domain name active or not. If you want to keep the domain but remove the site, just delete the files in public_html or remove the entire folder from File Manager. The domain stays registered and pointed to your hosting, so you can reuse it later without reconfiguration.

If you want to get rid of the domain entirely, do not rely on deleting the folder. Go to the Domains section and either cancel the domain (if you bought it through Hostinger) or let it expire. If you also want to stop paying for the hosting plan itself, you need to cancel that separately through Billing.

Our guide on how to cancel a Hostinger subscription walks through the exact steps, including what happens to your files.

Second, consider whether any email accounts are tied to that domain. If you are deleting the site but keeping the domain, email carries on fine. If you are deleting the domain entirely, you must download any important emails before the domain disappears because the email accounts will stop working once the domain registration is cancelled.

Third, think about backups. If the site in the domains folder contains any data you might need later (even old files or templates), download them first. Once you delete the folder, the content is gone unless you have a backup in the Hostinger dashboard backup system or an off-site copy.

For most users, the cleanest approach is:

1. Back up any files you want to save.
2. If you are done with the site, remove the website from the Websites dashboard (this disassociates the domain from the hosting plan and optionally deletes the folder).
3. If you want to keep the domain but start over, just empty the public_html folder.
4. Handle domain renewal and email accounts separately if needed.

This flow keeps your Hostinger account tidy without accidentally canceling a domain you still want.

Frequently Asked Questions

When I delete the folder from File Manager, can I get the files back later if I change my mind?

No. Deleting from File Manager or FTP sends the files to the trash (if you use the hPanel trash feature) or directly removes them permanently. Hostinger retains server backups for a limited time depending on your plan, typically 7 days for Business and Cloud plans, but not for the Single Shared Hosting plan.

Check your backup section in hPanel. If you have an active backup from before the deletion, you can restore it. Otherwise, the files are gone.

Will deleting the website folder also remove the domain from my domain list?

No. The Domains list shows registered domains regardless of whether they have a hosted website folder attached. The domain lives at the account level, not inside the folder.

You need to use the Domains section to remove the domain registration itself.

Can I delete a website that is only in the domains folder without logging into hPanel?

If you have FTP credentials, you can connect via an FTP client (like FileZilla) and delete the folder that way. The same rules apply. FTP cannot access the Websites dashboard, so you would only be deleting files, not the domain association.

If you also want to remove the domain from hosting, you need to log into hPanel.

Does deleting the website affect my Hostinger plan’s resource usage?

Yes, in a small way. Each domain folder uses a negligible amount of disk space and inode count. Deleting an unused folder frees up those resources.

It does not affect your plan’s bandwidth, processing power, or the number of websites you can host (since that limit is based on how many are linked, not how many folders exist). If you are hitting a file inode limit, removing unused folders can help.

Next Steps

If you have a domain in your Hostinger account that you want to keep but you are done with the current site, the fastest route is to delete the files from public_html using the File Manager. That keeps the domain active and ready for future projects.

If you are planning to start a new hosting account or upgrade your plan, using a coupon code can reduce the cost. Hostinger runs regular promotions, and you can find active deals through our coupon page. For first-time domain registrations, our domain coupon code for first-time users might help if you decide to register a new domain instead.

And if you are comparing Hostinger with other hosts and want to see how domain management differs, our comparison of Hostinger web hosting vs cloud hosting covers the key differences in how domains and files are organized across those plan types.

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