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Troubleshooting Let's Encrypt SSL Certificate Issues in cPanel

Last updated on Aug 08, 2025

Troubleshooting Let's Encrypt SSL Certificate Issues in cPanel

**Description:**A step-by-step guide for Brixly shared hosting customers to resolve common Let's Encrypt SSL certificate installation and renewal problems, including issues that arise after domain changes. This guide is suitable for users with basic technical knowledge and focuses on solutions you can implement directly in cPanel.

Table of Contents

Introduction

Let's Encrypt provides free SSL certificates for your website, which can be easily managed from your cPanel account. Most SSL issues can be resolved without server administrator access by following a few straightforward steps.

Common SSL Issues and Resolutions

1. Certificate Fails to Install

Possible Causes:

  • DNS not pointing to the correct server
  • HTTP validation failing (site not accessible at http://yourdomain.com)
  • Domain recently added or changed

Steps to Resolve:

  1. Check DNS Propagation
    • Use tools like DNS Checker to confirm your domain points to Brixly’s server IP.
    • DNS changes can take up to 24 hours to propagate.
  2. Verify Site Accessibility
    • Visit http://yourdomain.com and ensure the website loads. Let's Encrypt requires your site to be accessible over HTTP for validation.
  3. Re-attempt Installation
    • Log in to cPanel.
    • Go to SSL/TLS Status or Let's Encrypt SSL (depending on your cPanel theme).
    • Select your domain and click Run AutoSSL or Issue.
  4. Remove Old/Conflicting Certificates
    • In SSL/TLS Status, remove any expired or failed certificates before retrying.

2. SSL Not Displaying on Website (Still Shows as Not Secure)

Possible Causes:

  • SSL not installed correctly
  • Site still loading via HTTP
  • Mixed content (HTTP resources on HTTPS page)

Steps to Resolve:

  1. Force HTTPS:
    • In cPanel, open Domains.
    • Turn on the Force HTTPS Redirect for your domain.
  2. Check for Mixed Content:
    • Use your browser’s developer tools (Console tab) to identify any insecure resources.
    • Update links in your code or CMS to use https:// instead of http://.
  3. Clear Browser Cache:
    • Sometimes browsers cache old connection types; clear your browser cache and refresh.

3. Renewal Problems

Possible Causes:

  • DNS or domain issues
  • Renewal blocked by incorrect validation

Steps to Resolve:

  1. Check Domain Status:
    • Ensure the domain is active and not expired.
  2. Verify DNS Settings:
    • Your domain’s A record must point to your hosting server.
  3. Run AutoSSL Manually:
    • Go to SSL/TLS Status.
    • Click Run AutoSSL to trigger a manual renewal.
  4. Check Email Notifications:
    • Brixly may send alerts if renewal fails. Follow any instructions provided.

4. Conflicts After Domain or DNS Changes

Common Scenarios:

  • You’ve added or removed subdomains.
  • Domain was migrated or DNS settings changed.

Steps to Resolve:

  1. Re-check DNS:
    • Confirm all relevant A and CNAME records are correct.
  2. Re-issue the Certificate:
    • Go to SSL/TLS Status.
    • Select the affected domain and click Run AutoSSL.
  3. Remove Old Certificates:
    • Remove certificates linked to domains/subdomains that no longer exist.
  4. Wait for Propagation:
    • After DNS changes, allow time for changes to take effect before retrying.

General Troubleshooting Steps

  • Use Incognito/Private Browsing: This prevents cached SSL errors from affecting your tests.
  • Check with Online Tools: Use SSL Labs’ SSL Test to analyze your domain’s SSL status.
  • Update CMS Settings: Ensure your site’s base URL is set to https:// in WordPress, Joomla, etc.

Useful Tools in cPanel

  • SSL/TLS Status: Manage and view certificate status, run AutoSSL.
  • Let's Encrypt SSL: Direct interface for issuing and renewing Let's Encrypt certificates (if available).
  • File Manager: To edit .htaccess for redirects or fix mixed content issues.
  • Zone Editor: Manage DNS records for your domains.

Example .htaccess Rule to Force HTTPS:

RewriteEngine On
RewriteCond %{HTTPS} off
RewriteRule ^(.*)$ https://%{HTTP_HOST}%{REQUEST_URI} [L,R=301]

When to Contact Support

Contact Brixly support if:

  • You have tried all the above steps and your SSL still won’t install or renew
  • You see persistent errors such as “AutoSSL failed to assign a certificate”
  • Your domain is inaccessible or you receive unusual validation errors

Include the following details in your support ticket:

  • Your domain name
  • Steps you have already taken
  • Any error messages from cPanel or browser

By following this guide, most Let’s Encrypt SSL certificate issues can be resolved independently. For persistent issues, our support team is ready to help!