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How to Configure HTTPS and Subdomains on Apache for Ubuntu

A practical Ubuntu guide to DNS preparation, Apache name-based VirtualHosts, Certbot HTTPS certificates, independent subdomains, redirects, and renewal troubleshooting.
Length14 min Posted Quest giverVGSources Team
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Configure HTTPS on an Ubuntu Apache server in this order: point every hostname at the server in DNS, create a separate name-based VirtualHost for each site, enable and validate those hosts, then use Certbot’s Apache plugin to obtain one certificate covering the required names. Test both HTTPS routing and HTTP behavior, and verify automatic renewal with a dry run. A subdomain can serve a completely different site when its ServerName and DocumentRoot are defined in their own VirtualHost.

What you need before changing Apache

Have a registered domain, administrative access to the Ubuntu server, and control of the domain’s DNS zone. Let’s Encrypt is a free, automated certificate authority trusted by major browsers and clients, but it can issue a certificate only after it proves control of each requested hostname. For ordinary HTTP-01 validation, the hostname must resolve publicly to this server and Apache must be reachable on TCP port 80.

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  • Create an A record for the IPv4 address of the server and, when IPv6 is configured correctly, an AAAA record for the IPv6 address.
  • Create records for the apex name and every subdomain you will request, such as example.com, www.example.com, and app.example.com.
  • Allow inbound TCP 80 and 443 in both Ubuntu’s firewall and any cloud or datacenter security group in front of the machine.
  • Make sure the DNS records have propagated before asking the certificate authority to validate them.

An incorrect or stale AAAA record is a common cause of apparently mysterious failures: a validator may reach an IPv6 address where Apache is not configured, even though the A record is correct. Check every hostname from an external resolver and confirm that all returned addresses belong to this server. If you publish both record types, both paths should reach the same intended Apache service.

Make a list of the exact names users will visit before you begin. A certificate for example.com does not automatically cover www.example.com or app.example.com, and a DNS record by itself does not configure Apache. Keeping the DNS, VirtualHost, and certificate name lists identical prevents most setup errors.

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Plan the hostnames and certificate scope

Decide which names should serve the main site and which should serve separate applications. Apache uses name-based virtual hosting: it selects a VirtualHost by the hostname supplied by the browser, then serves that host’s configured document root.

Use case Apache setting Certificate requirement
Main domain only ServerName example.com Certificate includes example.com
Main domain and an alias ServerName example.com plus ServerAlias www.example.com Both names must be requested or otherwise covered by the certificate
Independent subdomain site Separate host with ServerName app.example.com and its own DocumentRoot Certificate includes app.example.com
Many subdomains Optional Apache alias such as ServerAlias *.example.com A wildcard certificate requires DNS-01 validation; the alias alone does not create DNS records or certificate coverage

Putting several names on one certificate is normal. Certbot treats each -d argument as a name to include, and the additional names become Subject Alternative Names. Separate certificates can still be useful when sites have different ownership or renewal boundaries, but the Apache routing decision is made by VirtualHost configuration, not by the certificate.

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Use an explicit ServerName for every independent site. Use ServerAlias only when the alias should serve exactly the same application and files. A wildcard alias may catch unexpected hostnames, so it is generally less predictable than separate, named hosts. Remember that Apache’s wildcard matching does not provision DNS, issue certificates, or create applications for those names.

Create a document root and VirtualHost for each site

Prepare the directories

Create a directory that contains the public files for each site. Keeping separate roots prevents a request for one hostname from accidentally exposing another application’s files.

sudo mkdir -p /var/www/example.com/public
sudo mkdir -p /var/www/app.example.com/public

Place each site’s intended index file in its own public directory and set ownership and permissions according to the application’s deployment method. The critical Apache requirement is that the process can read the document root and traverse its parent directories. If the files are readable but a parent directory blocks traversal, Apache can still return a 403 error.

Keep logs separate as well. Distinct error and access logs make it possible to tell whether a request reached the intended host when several sites share one server.

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Create the main-domain host

Save a file such as /etc/apache2/sites-available/example.com.conf:

<VirtualHost *:80>
    ServerName example.com
    ServerAlias www.example.com
    DocumentRoot /var/www/example.com/public

    <Directory /var/www/example.com/public>
        AllowOverride All
        Require all granted
    </Directory>

    ErrorLog ${APACHE_LOG_DIR}/example-error.log
    CustomLog ${APACHE_LOG_DIR}/example-access.log combined
</VirtualHost>

ServerName is the canonical hostname. Add a ServerAlias only for names that should serve the same files. The directory block grants access to that root and permits per-directory rules through .htaccess with AllowOverride All; if the application does not use .htaccess, a more restrictive override policy may be preferable.

The port-80 host is needed even when the finished site will redirect visitors to HTTPS. It gives Apache a place to answer HTTP-01 challenges and provides a clear routing target while you test DNS and certificate issuance.

Create a separate subdomain host

Save /etc/apache2/sites-available/app.example.com.conf with a different root and separate logs:

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<VirtualHost *:80>
    ServerName app.example.com
    DocumentRoot /var/www/app.example.com/public

    <Directory /var/www/app.example.com/public>
        AllowOverride All
        Require all granted
    </Directory>

    ErrorLog ${APACHE_LOG_DIR}/app-error.log
    CustomLog ${APACHE_LOG_DIR}/app-access.log combined
</VirtualHost>

This is how you point a subdomain to a different Apache site: give it its own DNS record, ServerName, document root, and VirtualHost file. Do not rely on a wildcard ServerAlias to perform application routing; an explicit host is easier to audit and prevents an unintended hostname from landing on the wrong site.

The subdomain does not need to share the main site’s directory, aliases, or logs. It can use different rewrite rules and deployment permissions, provided its directory block grants Apache the access the application requires.

Enable hosts and check Apache’s selection

  1. Enable each configuration file: sudo a2ensite example.com.conf and sudo a2ensite app.example.com.conf.
  2. Check syntax before reloading: sudo apachectl configtest. Continue only when it reports Syntax OK.
  3. Inspect the loaded map of addresses and name-based hosts with Apache’s virtual-host diagnostic command: sudo apachectl -S. Confirm that each hostname is attached to the expected file and that an unintended default host is not first.
  4. Reload Apache after a successful check: sudo systemctl reload apache2.

At this stage, test the sites over plain HTTP. Requesting http://example.com and http://app.example.com should return content from their respective roots. Fix routing before attempting certificate issuance; Certbot’s Apache plugin searches the enabled VirtualHost blocks and needs a matching host.

Apache ships with a default virtual host that can serve as a template. On a multi-site server, however, do not assume that the default host is harmless: if no ServerName matches, Apache may answer with the first host for that address and port. The output of apachectl -S shows which file is first and helps explain an unexpected page.

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Install Certbot and request the certificate

Install Certbot and its Apache integration using the current Ubuntu package guidance. The Apache plugin can locate matching VirtualHost blocks in /etc/apache2/sites-enabled/, add the required TLS directives, and reload Apache after installation.

Request all names that should be covered together:

sudo certbot --apache -d example.com -d www.example.com -d app.example.com

Certbot will ask for an email address and agreement to the certificate authority’s terms, then offer redirect behavior when the Apache configuration permits it. Supplying multiple -d options places the names on one certificate as Subject Alternative Names. Include only hostnames whose DNS already points to this server and whose HTTP service is reachable.

The command can include just the apex and one subdomain, or every public name that should share the lineage. If you later add a hostname, request a certificate that includes the complete desired set rather than assuming the old certificate changes automatically.

If you do not want Certbot to edit Apache automatically, obtain the certificate with webroot mode instead:

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sudo certbot certonly --webroot -w /var/www/example.com/public -d example.com -d www.example.com

In webroot mode, Certbot writes a temporary challenge file below the specified root. Apache must serve that path without application rewrites or authentication blocking it. You then reference the resulting certificate files in your own TLS VirtualHost configuration. This approach gives you manual control, but you must also ensure that your configuration reloads Apache after a successful renewal.

Understand HTTP-01 and DNS-01 validation

Validation method What must work When to choose it
HTTP-01 Public DNS resolves to the server and inbound TCP 80 reaches Apache, including the ACME challenge path Standard public websites where port 80 can remain reachable
DNS-01 A required _acme-challenge TXT record is created in DNS Port 80 cannot be reached, the service is not directly exposed, or a wildcard certificate such as *.example.com is required

HTTP-01 is usually the simplest choice for a normal public site. A port-80 redirect to HTTPS does not remove the need for port 80: the challenge request must still reach the ACME handler. If HTTP-01 cannot work, use an appropriate DNS-01 plugin and create the TXT record requested by Certbot. DNS-01 proves control of the DNS zone and is the validation method required for wildcard names.

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An Apache declaration such as ServerAlias *.example.com only changes how Apache matches requests that arrive. It does not create DNS records for arbitrary subdomains and does not make those names appear on a certificate. A wildcard certificate covers names in the wildcard’s scope, but it still does not make a nonexistent DNS name resolve.

When using DNS-01, update the authoritative DNS zone, not merely a local resolver or secondary interface. Wait for the TXT record to be visible publicly before retrying validation. For HTTP-01, verify the challenge URL through the same public path a certificate authority will use, including any load balancer, NAT rule, or edge firewall.

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Configure the HTTPS VirtualHosts and redirects

When you run certbot --apache, the plugin can add the TLS directives to matching hosts. Verify that each HTTPS hostname serves the intended document root and that the certificate lists the exact name in the browser’s certificate details.

If you want every HTTP request redirected to HTTPS, select Certbot’s redirect option when offered, or add an explicit port-80 redirect VirtualHost after the HTTPS site has been tested. Keep the ACME challenge path reachable during future renewals; an unconditional rewrite that blocks the challenge can make an otherwise valid renewal fail.

For a manually managed TLS host, the essential shape is:

<VirtualHost *:443>
    ServerName app.example.com
    DocumentRoot /var/www/app.example.com/public

    SSLEngine on
    SSLCertificateFile /etc/letsencrypt/live/app.example.com/fullchain.pem
    SSLCertificateKeyFile /etc/letsencrypt/live/app.example.com/privkey.pem

    <Directory /var/www/app.example.com/public>
        AllowOverride All
        Require all granted
    </Directory>
</VirtualHost>

The exact TLS module and site-enabling steps depend on the Ubuntu Apache package configuration; always run sudo apachectl configtest before reloading. Do not copy a certificate path from one certificate lineage to another: use the directory shown by Certbot for the certificate that covers the hostname.

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Test the HTTPS host directly before forcing redirects. Check the main domain and each subdomain separately, because a valid certificate on one name does not prove that Apache selects the right TLS VirtualHost for another name. Once each HTTPS response is correct, verify that an HTTP request receives the intended redirect and that the challenge URL remains an exception when HTTP-01 is in use.

Know where certificates are stored

Certbot maintains certificate lineages below /etc/letsencrypt/live/<domain>/. The important files are:

  • fullchain.pem: the server certificate followed by the required intermediate certificates.
  • privkey.pem: the private key; protect it from non-administrative users and do not publish it.

Apache should reference the files in the live directory rather than copying certificate material into a web root. Certbot updates the lineage during renewal, so a successful renewal followed by an Apache reload makes the new certificate available without changing your VirtualHost file.

Keep the private key readable only by the services and administrators that need it. If a manually maintained configuration points at a copied certificate elsewhere, renewal may update the live path while Apache continues serving the old copy.

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Verify automatic renewal

Let’s Encrypt certificates have a 90-day lifetime according to current Ubuntu Server guidance. Ubuntu documents a Certbot systemd timer that attempts renewal twice a day. The timer is not a substitute for testing: run a renewal simulation yourself.

sudo certbot renew --dry-run

A successful dry run confirms that the renewal method, DNS or HTTP challenge, and local Certbot configuration can complete without replacing the live certificate. Apache installations managed by Certbot are reloaded after a successful renewal. If you manage TLS directives yourself, verify that your deployment also reloads Apache after renewal.

Run the dry run after initial setup, after changing DNS, after changing redirects or firewall rules, and before relying on unattended renewal for production. Keep port 80 and the challenge path available for every hostname using HTTP-01. A timer that runs twice daily cannot fix a permanently broken DNS record, blocked port, or disabled VirtualHost.

Point a subdomain at a different Apache site

  1. Create app.example.com in DNS, pointing it to the server’s public address.
  2. Create /var/www/app.example.com/public and place the application files there.
  3. Create a dedicated VirtualHost whose ServerName is exactly app.example.com and whose DocumentRoot is that directory.
  4. Enable the file with a2ensite, run apachectl configtest, inspect apachectl -S, and reload Apache.
  5. Confirm the HTTP request reaches the new root, then request or reissue a certificate containing -d app.example.com.
  6. Test https://app.example.com before enabling an HTTP-to-HTTPS redirect for that host.

If the subdomain displays the main site, Apache is usually matching an earlier or default VirtualHost, the intended file is not enabled, or the request’s hostname does not match the configured ServerName/ServerAlias. The virtual-host map and separate access logs identify which configuration is receiving the request.

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If the browser reports a certificate-name warning while the HTTP page is correct, routing and certificate scope are out of sync. Add the exact hostname to the certificate request, then confirm that the HTTPS VirtualHost uses the renewed lineage and that Apache was reloaded.

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Troubleshoot issuance, routing, and renewal

DNS does not resolve to this server

Check A and AAAA answers for every requested name from outside the server’s network. Correct stale records, missing records, or an IPv6 address that does not accept the connection. Wait for the DNS change to propagate, then retry validation. Do not test only the apex name when the certificate request also contains www or an application subdomain.

Port 80 or 443 is blocked

Check both layers of filtering: the Ubuntu host firewall and the provider’s cloud security group or edge firewall. HTTP-01 specifically needs inbound port 80; HTTPS service needs port 443. If port 80 cannot be exposed, use DNS-01 rather than repeatedly retrying HTTP-01.

Apache reports a configuration error

Run sudo apachectl configtest and fix the first reported error before reloading. Common causes include a misspelled directive, an unmatched configuration tag, a nonexistent document root, or a certificate path that does not exist. Use sudo apachectl -S to find duplicate or unexpected host definitions.

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The wrong site answers

Confirm the browser is requesting the intended fully qualified hostname, the VirtualHost file is present in /etc/apache2/sites-enabled/, and its ServerName is exact. Review the host-specific access log and disable an obsolete default site only after confirming that no required host depends on it.

Renewal fails after a redirect or application change

Run sudo certbot renew --dry-run and inspect whether the challenge URL can still be served. For HTTP-01, temporarily remove rules that block the ACME challenge path or ensure the redirect allows the challenge handler to answer. For DNS-01, verify that the plugin can create the required _acme-challenge TXT record and that the authoritative DNS zone is the one being updated.

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The certificate is valid but the browser still warns

Check the hostname in the address bar character for character, including www and each subdomain. Inspect the served certificate and compare its names with the request. Then check which TLS VirtualHost answered with apachectl -S; a correct certificate installed on the wrong host can look like a certificate problem when it is actually a routing problem.

Final production checklist

  • Every certificate name has a working A or AAAA record pointing to the server.
  • TCP 80 and 443 are allowed wherever the chosen validation and service require them.
  • Each site has the correct ServerName, optional aliases, and document root.
  • All intended site files are enabled under /etc/apache2/sites-enabled/.
  • sudo apachectl configtest returns Syntax OK.
  • sudo apachectl -S shows the expected name-based hosts.
  • The requested certificate includes every hostname users will visit.
  • HTTPS serves the intended site for the main domain and each subdomain.
  • HTTP behavior is deliberate: either the site remains available for validation or redirects while preserving the ACME challenge path.
  • sudo certbot renew --dry-run completes successfully.

Frequently Asked Questions

How do I configure HTTPS for Apache on Ubuntu?

Point the domain’s DNS records to the Ubuntu server, allow TCP 80 and 443, create and enable a matching Apache VirtualHost, run sudo apachectl configtest, and request the certificate with sudo certbot --apache -d example.com. Test the HTTPS host and then verify renewal with sudo certbot renew --dry-run.

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How do I add HTTPS to an Apache subdomain?

Create a DNS record for the subdomain, define a VirtualHost with that exact ServerName and its own document root, enable it, and include the subdomain in Certbot’s request, for example -d app.example.com. Confirm that the HTTPS VirtualHost serves the subdomain’s files.

How do I point a subdomain to a different Apache site?

Give the subdomain its own DNS record, directory, VirtualHost file, ServerName, DocumentRoot, and logs. Enable the file, run apachectl -S to confirm Apache’s host map, reload Apache, and test the subdomain before issuing its certificate.

Do I need a separate certificate for every subdomain?

No. Certbot can place the apex domain and multiple subdomains on one certificate by supplying multiple -d options. Every hostname users visit must still be included, or covered by an appropriate wildcard certificate.

Can a wildcard ServerAlias provide HTTPS for all subdomains?

No. ServerAlias *.example.com only changes Apache request matching. It does not create DNS records or certificate coverage. A wildcard certificate such as *.example.com requires DNS-01 validation.

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What if port 80 is unavailable?

HTTP-01 validation normally requires inbound port 80. If that port cannot reach Apache, use DNS-01 validation and create the required _acme-challenge TXT record. DNS-01 is also required for wildcard certificates.

Where does Certbot store the Apache certificate and key?

Certbot maintains certificate lineages under /etc/letsencrypt/live/<domain>/. Apache normally uses fullchain.pem for the certificate chain and privkey.pem for the private key. Keep the key protected and out of web roots.

How often should I test Let’s Encrypt renewal?

Ubuntu documents a systemd timer that attempts renewal twice daily, while Let’s Encrypt certificates last 90 days. Run sudo certbot renew --dry-run after setup and after changes to DNS, redirects, firewalls, or VirtualHosts.

The Bottom Line

Reliable Apache HTTPS setup is a coordination task: DNS must point every name to the server, each name needs an unambiguous VirtualHost, and the certificate must list every hostname users request. Use HTTP-01 when port 80 is reachable, DNS-01 for blocked servers or wildcards, preserve the ACME challenge path, and prove unattended renewal with sudo certbot renew --dry-run.

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