How to Remove a Subdomain in ISPConfig

This guide shows you how to remove a subdomain, such as blog.yourdomain.com, from the ISPConfig control panel on your Noiz hosting account, and what that removal actually changes on the server. It is a two-click job, but what happens behind those two clicks depends on which kind of subdomain you created in the first place: one kind leaves every file where it was, another can delete a folder and everything inside it without a second prompt. If you are creating a subdomain rather than removing one, see How to Create a Subdomain in ISPConfig.

Last reviewed: 27 July 2026, against the current ISPConfig release. This guide is written for Noiz hosting and is kept current against ISPConfig. It complements, and does not replace, the official ISPConfig documentation linked below.

Official Documentation Reference

• Subdomains (ISPConfig 3 Documentation): a short primer on the two ways a subdomain can be created. It covers creating them only, which is why the removal behaviour is set out here rather than referred onwards.
• DNS Basics (ISPConfig 3 Documentation): background on the DNS side, which ISPConfig keeps in a separate module from the website.
• ISPConfig user manual: the field-by-field reference for the panel's forms, including the Web folder field that decides whether your files survive a removal.

Prerequisites

• You can log in to the ISPConfig control panel. The panel address for your account is in your Noiz welcome email and in the client area.
• A copy of anything on the subdomain you might want again, taken before you start. Deletion happens immediately, there is no undo and no recycle bin in the panel.
• Access to wherever the domain's DNS is managed, if you want the address to stop resolving as well.

Work Out Which Kind of Subdomain You Are Removing

ISPConfig can hold the same name, blog.yourdomain.com, in three different places, and each is removed from a different list. Open the Sites module and check them in this order:

• Websites > Subdomain for website: a standard subdomain, attached to a parent website and sharing its content or redirecting elsewhere. It has no document root of its own, only a Redirect Type and Redirect Path; everything else comes from the parent.
• Websites > Subdomain (Vhost): a vhost subdomain, which has its own document root, its own PHP settings and possibly its own SSL certificate. This menu item only appears when vhost subdomains are switched on for the server and your plan allows subdomains.
• Websites > Website: a full website that happens to be named after a subdomain. Removing this is removing a website, not a subdomain, and it takes the whole site with it.

Each list has a filter row under the column headings. Select the parent site in the Website drop-down, or type part of the name into the search box in that same row and click the filter button, rather than paging through a long list.

If the name is in none of those three lists, look at Aliasdomain for website and Aliasdomain (Vhost), and at the Auto-Subdomain setting on the parent website. A parent site set to the wildcard option (*.) answers on any subdomain that is not configured elsewhere, so the address can work without a subdomain record existing for it in Sites at all. In that case there is nothing to remove; change the parent website's Auto-Subdomain setting instead.

Remove the Subdomain

Both kinds are removed the same way, from the list rather than from the edit form. The edit form normally carries only Save and Cancel, so if you have opened the record and cannot find a delete button, go back to the list.

1. Open the Sites module and click Subdomain for website or Subdomain (Vhost) in the left menu, as appropriate.
2. Find the row for the subdomain. Check the Website column, not just the name, if you host several domains that use similar names.
3. Click the red delete button at the right-hand end of that row.
4. ISPConfig asks Do you really want to delete this record? and then deletes it. The prompt does not repeat the name back to you, so satisfy yourself that you are on the correct row before you click it.

The entry disappears from the list at once, but the web server configuration is rewritten a moment later by a background job. Watch for the red change indicator near the top of the panel, which lists changes not yet applied to the server. It normally clears in under a minute.

The subdomain also goes back into your plan's subdomain allowance, so you can create another one straight away.

What Happens to the Files

This is the part worth reading before you click delete rather than after.

A standard subdomain never had a folder of its own. It was only an extra name on the parent website's configuration, so removing it touches no files whatsoever. The parent website's configuration is simply rebuilt without that name, and everything on disk stays exactly as it was.

A vhost subdomain is different, and the outcome depends on the value that was typed into its Web folder field when it was created. Open the subdomain first and read that field:

• A path whose first segment is exactly web, so web on its own or something under it such as web/blog: the folder and its contents are deliberately left in place. That path sits inside the parent website's public directory, and ISPConfig refuses to delete anything there in case it takes the parent site down with it. Your files survive, they keep counting towards your disk quota, and they may still be reachable through the parent site at an address such as yourdomain.com/blog/. Delete them yourself over FTP or SSH if you want them gone. Read that first segment carefully, because it has to be web and nothing else: a folder named webshop or web2 is a different segment and gets none of this protection.
• Anything else, for example blog, which sits alongside the parent site's public directory rather than inside it: ISPConfig deletes that folder and everything in it, then works upwards removing now-unused parent folders, stopping as soon as it reaches one that another vhost subdomain or vhost alias on the same website still uses. This is permanent and there is no confirmation beyond the single prompt you already answered.

Two subdomains created on the same afternoon can therefore behave completely differently on removal, so take a copy of anything you care about first.

Removing a vhost subdomain also clears its own web server configuration, its PHP handler and its log directory, along with any folder protection set against the subdomain itself. The generated web statistics pages sit inside the web folder, so they live or die by the rule above rather than being removed separately. It does not remove databases, FTP accounts, shell users or cron jobs, which belong to the parent website. If any of those only existed to serve the subdomain, tidy them up in the relevant list.

What Happens to the SSL Certificate

Any certificate that covered the subdomain stops covering it. What that looks like depends on the kind of subdomain.

For a standard subdomain on a parent website using a free certificate, the subdomain was one of the extra names on the parent's certificate, and removing it makes ISPConfig request a fresh certificate for the parent site straight away without that name. Two things follow. If that request fails, typically because another name on the same site no longer resolves to the server, ISPConfig clears the Let's Encrypt SSL tick box on the parent website rather than leave a broken renewal in place, so check that box is still ticked afterwards; if it is not, fix the DNS for every name on the site, tick it again and save. See How to Secure a Website with a Free SSL Certificate in ISPConfig. Free certificate authorities also apply rate limits, so removing and recreating the same subdomain repeatedly in a short period can leave the parent site waiting for its next certificate. None of this applies if the subdomain had Don't add to Let's Encrypt certificate ticked, because it was never on the parent's certificate to begin with.

For a vhost subdomain, the certificate belonged to the subdomain and goes with it. Nothing on the parent website changes.

In both cases, if the subdomain's DNS record is still in place after removal, visitors typing the old address are likely to meet a certificate warning. That is expected, and the fix is to remove the DNS record, not to try to put a certificate back.

The DNS Record Is Yours to Remove

ISPConfig keeps websites and DNS in separate modules, and deleting a subdomain in Sites does not touch the DNS zone. The A or CNAME record for blog.yourdomain.com is still there afterwards, still pointing at the hosting server.

Left in place, that record does not produce a clean "site not found". The name still resolves, the request still reaches the server, and the server answers with whatever it treats as the default site, so visitors may land on an unrelated page or a placeholder. Remove the record wherever the zone actually lives:

• If the zone is in ISPConfig, open the DNS module and delete the record. See How to Manage DNS Records in ISPConfig.
• If the domain uses nameservers elsewhere, such as your registrar or another DNS provider, the record has to be removed there. The panel cannot reach it.
• If Noiz manages the DNS for the domain and you are not sure, open a support ticket with the exact name and it can be checked and removed for you.

One exception is worth knowing: if the parent website's Auto-Subdomain is set to the wildcard option, the web server answers for any name under the domain, so the old address keeps loading the parent site's content for as long as it still resolves. That is the wildcard doing its job, not a failed deletion. Removing the DNS record is still what stops it, unless the zone also holds a wildcard record, in which case the parent website's Auto-Subdomain setting is what has to change.

Email Addresses on the Subdomain Are a Separate Thing

A mailbox such as [email protected] has nothing to do with the website subdomain you just removed. Email lives in the Email module, under its own email domain record, and it is not created, changed or deleted when you add or remove a web subdomain.

So mail carries on. The mailboxes stay on the server and keep using disk space, webmail keeps working, and messages keep being delivered for as long as the MX and address records for the subdomain remain in DNS. If you want the email gone as well, remove it deliberately: open Email > Email Accounts > Domain, delete the mailboxes, aliases and forwards on that email domain, then remove the email domain itself. That works the other way round too, so removing an email domain has no effect on a website subdomain of the same name. See How to Create an Email Mailbox in ISPConfig for where these live in the panel.

Check That It Worked

1. The subdomain is gone from the list you deleted it in, and the red change indicator at the top of the panel has cleared.
2. The parent website still loads normally over HTTPS. This is the check people skip and the one that matters, because the removal rewrites the parent site's configuration and certificate.
3. The parent site's certificate no longer lists the subdomain. Click the padlock in your browser and view the certificate, or run this from any machine with the openssl tools installed:

openssl s_client -connect yourdomain.com:443 -servername yourdomain.com < /dev/null 2>/dev/null | openssl x509 -noout -text | grep -A1 "Subject Alternative Name"

dig +short blog.yourdomain.com

Replace yourdomain.com and blog.yourdomain.com with your own names. The first command lists every name the live certificate covers, and the removed subdomain should not appear. The second shows whether the old address still resolves, which tells you whether a DNS record is left to tidy up.

Troubleshooting

• The subdomain is not in the Subdomain for website list: it was created as a Subdomain (Vhost), as a full Website, or as an aliasdomain. Check each list in turn. If the account holds many sites, use the filter row rather than scrolling.
• The delete button does nothing, or you get a permissions error: your login may not own that record, for example if the site sits under a different client account. Open a support ticket rather than working around it.
• The address still loads the old content: check the parent website's Auto-Subdomain setting for the wildcard option, then retry in a private window. Browsers hold on to redirects and DNS answers for a long time.
• The address shows an unrelated site or a certificate warning: the DNS record is still pointing at the server. Remove the record as described above.
• Disk usage has not gone down: the vhost subdomain's Web folder had web as its first segment, so its files were deliberately left in place. Delete the folder yourself over FTP or SSH once you are sure of the contents.
• The parent website lost its free certificate: the certificate request that followed the removal failed. Make sure every name still attached to that site resolves to the server, then re-enable Let's Encrypt SSL on the parent website and save.
• Email to the subdomain still arrives: expected. The email domain is a separate record in the Email module and has to be removed there.
• You deleted the wrong one: recreate it with the same settings, then restore the files from your own backup. Recreating the record does not bring content back.

Need a Hand?

If you are on a managed Noiz plan, or you are not certain whether a subdomain is safe to remove, open a ticket from your Noiz client area before you delete anything. Include the full subdomain name, the parent website it belongs to, and whether you want the files and the DNS record removed as well, and the support team will handle it for you.