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To rekey an SSL certificate on Apache running Ubuntu, generate a new private key and CSR, obtain a newly signed certificate containing every required hostname, install the certificate and intermediate chain, point the correct HTTPS VirtualHost at the new files, verify that the certificate matches the new key, and reload Apache. Keep the old key, certificate, and configuration available until the replacement has been tested in production.
The procedure below covers both a manually issued certificate and an ACME deployment managed by Certbot, including the checks that prevent the most common Apache start-up failures.
What rekeying changes
Rekeying is more than renewing an expiry date. A rekey creates a new private key and a new certificate-signing request (CSR). A certificate authority signs a certificate for that CSR, so the resulting certificate contains a different public key from the one in the old certificate. Apache must then be configured to use the new certificate and its matching private key.
If you only obtain another certificate for the existing key, you have reissued or renewed the certificate, not rekeyed it. Rekeying is appropriate after a suspected key exposure, when changing key parameters, or when your certificate authority requires a fresh key for a replacement certificate.
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Before you touch Apache
Confirm access and ownership
- Use an account with
sudoaccess on the Ubuntu server. - Identify every DNS name the service must answer, such as
example.comandwww.example.com. Modern certificates validate Subject Alternative Names (SANs); do not rely on the Common Name alone for hostname coverage. - Know which certificate authority will sign the CSR. A manual CA workflow and an ACME workflow have different issuance and renewal steps.
- Schedule a short change window if the key is encrypted and Apache requires an interactive passphrase during a restart.
Preserve a rollback set
Copy the current certificate, private key, chain file, and the relevant Apache site configuration to a root-owned backup location before generating anything. Keep the new key in a separate filename until issuance and verification are complete. Private keys should not be placed in a user home directory with broad read permissions.
Ubuntu commonly stores public certificates under /etc/ssl/certs and private keys under /etc/ssl/private. Certbot-managed material normally remains under /etc/letsencrypt/live/<domain>/. The exact paths in your enabled VirtualHost are authoritative.
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Apache can have several port-443 VirtualHosts, and editing the wrong one is a frequent cause of apparently unchanged certificates. First ask Apache which names and files are enabled:
sudo apache2ctl -S
sudo grep -R "SSLCertificate" /etc/apache2/sites-enabled/
sudo grep -R "<VirtualHost .*:443" /etc/apache2/sites-enabled/Open the VirtualHost that serves the hostname you will test. Record its ServerName, ServerAlias, SSLCertificateFile, SSLCertificateKeyFile, and any chain directive. Back up that site file and note whether it is a symlink from sites-available into sites-enabled.
Do not assume that the first certificate found by a recursive search is active. The name supplied through the TLS Server Name Indication (SNI) request selects a VirtualHost, so the test hostname, the certificate SAN, and the edited VirtualHost must all agree.
2. Generate a new private key and CSR
Use a protected working directory
Create the key where only root can read it, or set a restrictive umask before running OpenSSL:
sudo -i
umask 077
mkdir -p /root/tls-rekey-example.com
cd /root/tls-rekey-example.comThe traditional RSA example documented by Apache is:
openssl genrsa -des3 -out server.key 2048
openssl req -new -key server.key -out server.csrgenrsa -des3 encrypts the private key with a passphrase. When OpenSSL asks for the CSR Common Name, enter the server’s fully qualified domain name (FQDN), as Apache’s SSL/TLS FAQ advises. The CA’s request form or configuration must also include every required DNS name as a SAN. For example, a certificate intended for both example.com and www.example.com must list both names, not just one of them.
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On OpenSSL versions that support -addext, SANs can be supplied directly while creating the CSR:
openssl req -new -key server.key -out server.csr
-subj "/C=GB/ST=England/L=London/O=Example Ltd/CN=example.com"
-addext "subjectAltName=DNS:example.com,DNS:www.example.com"If that option is unavailable, use the CA’s documented CSR configuration or web form to request SANs. Inspect the finished CSR before submitting it:
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openssl req -in server.csr -noout -subject -textKeep server.key secret and send only server.csr to the certificate authority. Never email or upload the private key as part of a certificate request.
Passphrase trade-off
An encrypted key reduces the impact of a stolen key file, but Apache may need the passphrase whenever the service starts. Apache warns that “Removing the pass-phrase removes a layer of security from your server – proceed with caution!” Ubuntu similarly describes an unattended service without a passphrase as convenient but insecure because compromise of the key compromises the server. If unattended startup requires an unencrypted key, restrict it to root with mode 600, keep an encrypted backup offline, and protect the server itself.
3. Obtain the newly signed certificate
Manual certificate-authority issuance
Submit server.csr through the chosen CA’s issuance process. Complete any required domain-control validation, then download the server certificate and the intermediate certificate or chain file. Confirm that the issued certificate contains the same SAN set you requested and that its public key corresponds to the new CSR.
ACME issuance with Certbot
For a conventional Apache site, Ubuntu documents this command:
sudo certbot --apache -d example.com -d www.example.comPass every required hostname explicitly. Certbot’s Apache plugin locates the matching VirtualHost, typically in /etc/apache2/sites-enabled/, adds the necessary TLS directives, and reloads Apache. In a nonstandard topology, use the CA’s documented DNS-01 challenge or a centralized ACME workflow; DNS-01 may require access to the DNS provider’s API and is commonly used when the server cannot answer an HTTP challenge.
Certbot stores the managed files beneath /etc/letsencrypt/live/<domain>/. In that layout, fullchain.pem contains the server certificate followed by its intermediate certificates, while privkey.pem is the private key. Reference the paths Certbot supplies instead of copying files into a second location that automated renewal will not update.
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Manual CA or Certbot: which workflow fits?
| Decision point | Manual CSR and CA issuance | Certbot with ACME |
|---|---|---|
| Issuance | You generate and submit a CSR, complete the CA’s validation, and install the returned files. | Certbot requests a certificate and completes an ACME challenge, often through the Apache plugin. |
| Hostname coverage | You select SANs in the CA request and must verify the issued names. | Every required name is passed with a -d option; wildcard certificates generally require a DNS-01 workflow. |
| Renewal | You track expiry, create replacement CSRs when required, and schedule installation yourself. | Certbot can automate renewal; test the renewal path with sudo certbot renew --dry-run. |
| File layout | Common system paths are /etc/ssl/certs for certificates and /etc/ssl/private for keys, subject to your configuration. |
Managed files are under /etc/letsencrypt/live/<domain>/, including fullchain.pem and privkey.pem. |
| Reload behavior | You run apache2ctl configtest and reload or restart Apache after installing files. |
The Apache plugin writes directives and reloads during issuance; a deployment hook can be used when your topology needs a separate reload. |
| DNS or API access | Usually limited to the CA validation method you select. | HTTP challenges can work through Apache; DNS-01 requires control of the relevant DNS zone or its API. |
| Private-key control | You create and retain the key locally and send the CA only the CSR. | Certbot also generates and stores the key locally, but its permissions and renewal automation must be included in your operational controls. |
4. Install the certificate, key, and chain
Manually issued files
Place the files in protected locations, preserving ownership and modes. Adapt the source names to the files returned by your CA:
sudo install -o root -g root -m 644 new.crt /etc/ssl/certs/example.com.crt
sudo install -o root -g root -m 600 new.key /etc/ssl/private/example.com.key
sudo install -o root -g root -m 644 issuer-chain.pem /etc/ssl/certs/issuer-chain.pemIn the HTTPS VirtualHost, use the new paths:
SSLCertificateFile /etc/ssl/certs/example.com.crt
SSLCertificateKeyFile /etc/ssl/private/example.com.key
# Use this only when your Apache configuration expects a separate chain file:
SSLCertificateChainFile /etc/ssl/certs/issuer-chain.pemApache’s documented primary directives are SSLCertificateFile and SSLCertificateKeyFile. Depending on Apache version and configuration, the intermediate certificates may be supplied separately with SSLCertificateChainFile or appended after the server certificate in a full-chain file. Follow the syntax supported by the installed Apache package; do not append an unrelated root certificate merely to make a file longer.
Certbot-managed files
Point Apache at the paths in the domain’s Certbot directory, for example:
SSLCertificateFile /etc/letsencrypt/live/example.com/fullchain.pem
SSLCertificateKeyFile /etc/letsencrypt/live/example.com/privkey.pemfullchain.pem already combines the leaf certificate and intermediate certificates. Do not replace it with only the leaf certificate, or clients that do not already cache the intermediate may report an incomplete chain. Leave the files under Certbot’s control so subsequent renewals update what Apache reads.
5. Prove that the certificate and key match
Perform these checks before changing live traffic. For an RSA key, Apache documents comparing the modulus digests:
openssl x509 -noout -modulus -in new.crt | openssl md5
openssl rsa -noout -modulus -in new.key | openssl md5The two resulting digests must be identical. The MD5 output here is a convenient equality check for the public modulus, not a claim that MD5 is suitable for signing or protecting data. If the values differ, stop: installing that pair will cause Apache to fail or serve the wrong key. Locate the key generated for the CSR and repeat the issuance process if necessary.
Inspect the certificate’s identity and lifetime:
openssl x509 -in new.crt -noout -subject -issuer -dates -ext subjectAltNameCheck that the subject, issuer, notBefore, notAfter, and every SAN are what you expect. A certificate that matches the key but omits a required hostname is still unusable for that hostname.
Validate the chain with Ubuntu’s trust bundle and the intermediate file:
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openssl verify
-CAfile /etc/ssl/certs/ca-certificates.crt
-untrusted issuer-chain.pem new.crtThe trust-store path can vary by Ubuntu release, and a Certbot full chain should be tested using the files in its managed directory. A successful result means the leaf can be built to a trusted root with the supplied intermediates; it does not replace an end-to-end test from a client.
6. Enable SSL and reload the correct site
If SSL support is not enabled, enable the module. Enable the HTTPS site only if it is not already active:
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sudo a2ensite example.com-ssl.confUse the actual filename shown in /etc/apache2/sites-available; enabling a different file can create a second VirtualHost that hides the problem rather than fixing it.
Always parse the complete configuration before asking systemd to reload Apache:
sudo apache2ctl configtest
sudo systemctl reload apache2Proceed only when configtest reports Syntax OK. Reloading lets existing connections finish while new connections use the new certificate. If reload is unavailable, or an encrypted private key requires an interactive passphrase, use the documented restart path and provide the passphrase through the server’s secure console or service mechanism. Do not put the passphrase in a shell command, unit file, or publicly readable script.
7. Test what Apache actually serves
Check from the server
Request the endpoint with the hostname that selects the intended SNI VirtualHost:
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openssl s_client -connect example.com:443 -servername example.com -showcerts </dev/nullReview the returned subject, SANs, issuer, validity dates, and certificate chain. The -servername option is essential when the server hosts multiple HTTPS names; without it, you may test the default VirtualHost instead of the one you edited.
Check from an independent client
Test from a workstation or monitoring system outside the server’s network as well. This catches load balancers, reverse proxies, CDN edges, or DNS records that still point to another machine. Confirm that every required hostname resolves to the intended endpoint and that clients receive the new certificate, not merely that Apache accepted the file.
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Exercise Certbot renewal
For a Certbot-managed deployment, run:
sudo certbot renew --dry-runThis performs a renewal test without replacing the live certificate. Treat a failed dry run as an operational issue to resolve before the current certificate expires; inspect challenge access, DNS permissions, renewal configuration, and Apache reload hooks.
Why Apache fails after a replacement
“Private key does not match certificate”
The modulus digests differ, or the VirtualHost points to an old key while the certificate path was changed. Recheck both directives and repeat the equality test against the exact files Apache reads.
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“Permission denied” or an unreadable key
The Apache service account must be able to read the private key through its directory path, while unrelated users must not. Keep the key root-owned with restrictive mode, verify directory permissions, and check whether a security policy is blocking access. Do not solve the problem by making the key world-readable.
The old certificate is still displayed
You may have edited an inactive site, omitted the SNI name in your test, or left a proxy and load balancer serving the old certificate. Run apache2ctl -S, compare the requested hostname with ServerName/ServerAlias, and test the public endpoint from outside the host.
Hostname or SAN warning in clients
The replacement certificate does not list the requested DNS name, or the client is using an alias not included in the CSR. Obtain a corrected certificate with all required SANs and install it only after repeating the identity checks.
Incomplete chain errors
Apache may be sending only the leaf certificate, or the intermediates are in the wrong order. Use the CA-provided chain or Certbot’s fullchain.pem, then run openssl verify and inspect all certificates returned by openssl s_client -showcerts.
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Malformed PEM or passphrase prompt
Check that certificate files contain intact PEM headers and footers, such as -----BEGIN CERTIFICATE-----, with no accidental text added during copying. A key encrypted with a passphrase can also prevent an unattended reload or restart. Decide explicitly whether the service design supports an encrypted key; never remove encryption merely to silence a prompt without applying the corresponding permission and backup controls.
When Apache refuses to reload, read the service status and error log immediately:
sudo systemctl status apache2
sudo journalctl -u apache2 -n 100 --no-pager
tail -n 100 /var/log/apache2/error.logRollback and retirement
If the new endpoint fails validation, restore the backed-up certificate, key, chain, and VirtualHost configuration, run sudo apache2ctl configtest, and reload Apache. Keep the new files isolated until you understand the failure. Once the replacement has been observed serving correctly, renewal has been tested where applicable, and your rollback window has ended, dispose of obsolete private keys according to your organization’s key-destruction policy. Do not delete the old material merely because Apache accepted the new configuration.
Quick Recap
Operational checklist
- The active port-443 VirtualHost and all required hostnames are documented.
- The new private key was generated locally and was never sent to the CA.
- The CSR and issued certificate contain every required SAN.
- The certificate, key, and chain are installed at the exact paths referenced by Apache.
- Private-key ownership and permissions restrict access, and encrypted backups are stored offline when an unencrypted runtime key is necessary.
- Certificate and key equality was verified before activation.
apache2ctl configtestpassed before reload or restart.- An SNI-aware endpoint test confirms the new certificate, issuer, expiry, and chain.
sudo certbot renew --dry-runpasses for Certbot-managed certificates.- The previous certificate, key, and configuration remain available until production verification and rollback needs are complete.
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