During the deployment of SSL certificates for websites, many administrators encounter problems such as certificates failing to load correctly, browsers displaying untrusted certificate warnings, Nginx or Apache failing to start, and even web pages displaying errors and becoming inaccessible. These issues are often related to incorrect certificate file paths, incomplete certificate chains, conflicts between different certificates, uncleaned old configurations, or web services not correctly pointing to the SSL file. Because SSL involves multiple components such as key files, certificate files, and intermediate certificate chains, and different web servers have different configurations, troubleshooting must involve a systematic analysis from four perspectives: file integrity, permissions, certificate chain structure, and configuration paths, rather than simply relying on regenerating the certificate.

　　The most common source of failure during SSL deployment is incorrect certificate file path configuration. In many cases, administrators upload the certificate file to the server but use the wrong path during configuration, or different versions of certificate files are incorrectly overwritten. For example, a complete SSL configuration for Nginx typically includes a certificate file and a private key file:

ssl_certificate /etc/nginx/ssl/example.com/fullchain.pem;
ssl_certificate_key /etc/nginx/ssl/example.com/privkey.pem;

　　If the path does not exist, the file is empty, the file permissions are insufficient, or multiple sibling directories are mistakenly entered (such as example, example.com, example_ssl), Nginx will display an error message during startup, such as:

[emerg] cannot load certificate key "/etc/nginx/ssl/example.com/privkey.pem"

　　These types of problems can usually be resolved by checking the file path and verifying that the certificate corresponds to the key. Administrators can use the following command to check if the private key matches the certificate:

openssl rsa -noout -modulus -in privkey.pem | openssl md5
openssl x509 -noout -modulus -in cert.pem | openssl md5

　　If the output values ​​differ, it indicates a mismatch between the key and certificate, requiring the correct key to be regenerated or retrieved.

　　An incomplete certificate chain is another core reason for SSL deployment failure. Many free or wildcard certificates require a complete certificate chain; otherwise, while the browser can load the site, it will still display an "Untrusted Certificate Authority" message, especially noticeable on Android phones or some older systems. A complete chain typically includes the server certificate and intermediate certificates, assembled as follows:

cat cert.pem intermediate.pem > fullchain.pem

　　Both Nginx and Apache require `fullchain.pem`, not just `cert.pem`. A missing intermediate chain can lead to some DNS resolution errors, such as Chrome displaying `NET::ERR_CERT_AUTHORITY_INVALID`. The key to resolving this issue is ensuring that the fullchain file is used, not a separate certificate.

　　Certificate conflicts are particularly common in multi-domain, multi-site servers. If multiple sites' configuration files share the same port and `server_name` is not set correctly, Nginx may encounter certificate loading errors. For example, accessing `example1.com` might load the certificate for `example2.com`, causing the browser to report a domain mismatch. This situation is usually caused by incorrect `default_server` or `listen` configurations, such as:

listen 443 ssl;

　　The presence of multiple sites causes the system to be unsure which site should be the default, leading to incorrect certificate matching. The correct approach is to set `default_server` for only one default site.

listen 443 ssl default_server;

　　And add a unique server_name for each site:

server_name example.com www.example.com;

　　This allows Nginx to correctly assign certificates via SNI (Server Name Indication).

　　Another common reason for SSL deployment failure is the failure to clean up old certificate configurations. When modifying a new certificate, the administrator may have changed the main configuration file, but sub-configuration files or include files may still retain the old paths, causing duplicate loading of service configurations or certificate corruption. For example, in Apache, if an old certificate configuration is still loaded, the following error may occur:

AH02565: Certificate and private key example.com:443 do not match

　　The solution is to find the SSL configuration that is being called repeatedly:

grep -R "SSLCertificateFile" /etc/httpd/

　　Deleting or commenting out the relevant configuration section after finding the old certificate will avoid conflicts.

　　Permission issues are also a hidden reason why certificates fail to load. Many system security restrictions require that private key file permissions not exceed 600; otherwise, the web service will refuse to load it.

chmod 600 privkey.pem
chown root:root privkey.pem

　　In panel environments like Plesk or BT Panel, loading failures may occur because the panel maintains file permissions, potentially overwriting manually modified certificate paths. In this case, it's recommended to re-upload the certificate within the panel itself, rather than manually replacing the file via SSH.

　　In automated certificate systems like Let's Encrypt or acme.sh, certificate renewal failures can also cause the website to load the old certificate or the certificate to expire. Renewal failures may stem from incorrect domain name resolution, port 80 being occupied, or forced redirects blocking verification. For example, acme.sh will display the following message when it cannot verify the HTTP path:

Verify error:Fetching http://example.com/.well-known/acme-challenge

　　Solutions include disabling forced HTTPS, temporarily allowing Let's Encrypt authentication paths, or specifying DNS authentication for acme.sh. For example:

acme.sh --issue --dns dns_cf -d example.com

　　If the server has a reverse proxy, advanced WAF, or similar implementation, verification requests may be intercepted; therefore, it is essential to ensure the verification path is accessible.

　　In some cases, SSL deployment failure is not due to the certificate itself, but rather to a misconfigured Nginx or Apache system. For example, an outdated OpenSSL version that does not support certain newer algorithms, incorrect HTTP/2 activation, or incorrect configuration syntax can all prevent the certificate from being loaded. You can check for syntax issues by testing the configuration.

nginx -t
apachectl configtest

　　If you encounter an "undefined directive" error or a human error in the configuration, you need to fix each problem as prompted.

　　In addition, incorrect certificate formats often cause loading failures. For example, the complete certificate chain may contain extra spaces or a BOM header, or the certificate may not have been copied in PEM format.

-----BEGIN CERTIFICATE-----
...
-----END CERTIFICATE-----

　　Any actions that damage the file format may cause web service failures; it is essential to ensure that the file format is preserved intact.

　　In summary, SSL deployment failures can generally be categorized into several types: incorrect certificate path, incomplete certificate chain, certificate and key mismatch, multi-site certificate conflict, incorrect port pointing, insufficient permissions, old configuration not being deleted, automatic renewal failure, or incorrect web service configuration. During troubleshooting, it is recommended to analyze step-by-step from underlying files and matching relationships to service configuration, port listening, and finally system logs to quickly pinpoint the problem.

　　In the final stage, if the problem persists, you can directly check the error logs. The Nginx log path is typically:

/var/log/nginx/error.log

　　The Apache logs are as follows:

/var/log/httpd/error_log

　　If you encounter error messages like "PEM_read_bio" or "unsafe permissions," you can quickly pinpoint the source of the problem.

　　Through systematic troubleshooting and structured remediation, most certificate conflicts and path errors can be resolved quickly, ensuring your website successfully enables HTTPS encryption. After deployment, it is also recommended to regularly check certificate expiration dates, enable automatic renewal, and implement a certificate backup strategy in the production environment to avoid sudden access disruptions due to certificate expiration.