How to Backup Website Files

Backing up website files is one of the most critical yet frequently overlooked tasks in website management. Whether you run a personal blog, an e-commerce store, or a corporate landing page, your website contains valuable digital assets—HTML, CSS, JavaScript, images, configuration files, and custom scripts—that are essential to its functionality and identity. Losing these files due to server failure, hacking, accidental deletion, or software update errors can result in hours of downtime, lost revenue, damaged reputation, and irreversible data loss.

A comprehensive backup strategy ensures that you can restore your website to a fully operational state quickly and reliably. Unlike content backups (such as database exports), file backups preserve the entire structure of your website’s codebase and media assets. This tutorial provides a complete, step-by-step guide to backing up website files, covering best practices, recommended tools, real-world examples, and answers to common questions—equipping you with the knowledge to safeguard your digital presence effectively.

Step-by-Step Guide

1. Identify What Needs to Be Backed Up

Before initiating any backup process, determine exactly which files and directories require protection. Not all website components are equal, and backing up unnecessary files wastes storage space and time.

Typical website file components include:

• HTML, CSS, and JavaScript files – These define your site’s structure, styling, and interactivity.
• Media files – Images, videos, PDFs, audio files, and other uploads stored in folders like /wp-content/uploads/, /images/, or /assets/.
• Configuration files – Files like .htaccess (Apache), nginx.conf, wp-config.php (WordPress), .env (Laravel), or web.config (IIS) contain vital settings.
• Custom themes and plugins – Especially important for CMS platforms like WordPress, Joomla, or Drupal.
• Server-side scripts – PHP, Python, Node.js, or Ruby files that power dynamic functionality.
• SSL certificates and private keys – Often stored in /etc/ssl/ or similar directories on Linux servers.

Exclusions typically include cache folders (e.g., /wp-content/cache/), temporary files, logs, and system-generated files that can be regenerated. Always review your website’s structure and consult your hosting provider’s documentation to ensure you’re not missing critical directories.

2. Choose Your Backup Method

There are several ways to back up website files, each suited to different technical skill levels and hosting environments:

Method A: Manual Backup via FTP/SFTP

This method is ideal for users with basic technical knowledge and access to their website via FTP (File Transfer Protocol) or its secure variant, SFTP.

1. Install an FTP client such as FileZilla, Cyberduck, or WinSCP.
2. Enter your FTP credentials (hostname, username, password, and port—usually 21 for FTP or 22 for SFTP), which you can find in your hosting control panel.
3. Connect to your server and navigate to the root directory of your website (commonly public_html, www, or httpdocs).
4. Select all files and folders you identified in Step 1. Right-click and choose “Download” or “Get.”
5. Save the downloaded files to a secure, organized local folder on your computer—e.g., “WebsiteBackup_2024-06-15”.

Always verify the integrity of the downloaded files by comparing folder structures and checking that key files (like index.html or wp-config.php) are present and not corrupted.

Method B: Backup via Hosting Control Panel

Many web hosts (e.g., SiteGround, Bluehost, Hostinger) provide built-in backup tools within cPanel, Plesk, or custom dashboards.

1. Log in to your hosting account.
2. Navigate to the “Backup” or “Files” section.
3. Select “Download a Full Website Backup” or “Backup Website Files.”
4. Choose the destination (download to your computer or save to cloud storage).
5. Wait for the process to complete. Some hosts send an email notification when the backup is ready.
6. Download the .zip or .tar.gz file and store it securely.

While convenient, be aware that some hosts only offer partial backups or charge extra for full file backups. Always confirm the scope of what’s included.

3. Automate Backups Using Scripts

For advanced users or those managing multiple sites, automation ensures consistency and eliminates human error.

Linux/macOS: Using tar and cron

You can create a shell script to compress and archive your website files, then schedule it with cron.

Create a backup script named backup_website.sh:

!/bin/bash
DATE=$(date +%Y-%m-%d)
SOURCE="/var/www/html"
DESTINATION="/home/user/backups/website_$DATE.tar.gz"
tar -czf "$DESTINATION" "$SOURCE"
echo "Backup completed: $DESTINATION"

Make it executable:

chmod +x backup_website.sh

Test the script manually:

./backup_website.sh

Then schedule it to run daily using cron:

crontab -e

Add this line to run at 2 AM daily:

0 2 * * * /home/user/backup_website.sh

This method gives you full control and can be extended to upload backups to cloud storage (e.g., AWS S3, Google Drive) using tools like rclone or awscli.

Windows: Using PowerShell and Task Scheduler

On Windows servers, PowerShell can automate file compression and scheduling.

Create a script named Backup-Website.ps1:

$date = Get-Date -Format "yyyy-MM-dd"
$source = "C:\inetpub\wwwroot"
$destination = "C:\Backups\Website_$date.zip"
Compress-Archive -Path $source -DestinationPath $destination -Force
Write-Host "Backup completed: $destination"

Open Task Scheduler, create a new task, set the trigger to daily at a low-traffic time, and set the action to run PowerShell with the argument:

-ExecutionPolicy Bypass -File "C:\Scripts\Backup-Website.ps1"

Test the task manually before relying on it.

4. Store Backups Securely

Backing up files is only half the battle. Where you store them determines whether you can recover them when needed.

Never store backups on the same server as your live website. If the server is compromised or fails, your backups may be lost too.

Recommended storage options:

• Local external drives – Use encrypted USB or SSD drives. Label them clearly and store them in a fireproof safe.
• Cloud storage – Services like Google Drive, Dropbox, or Microsoft OneDrive offer easy access and versioning. Enable two-factor authentication.
• Offsite servers – Use a separate VPS or dedicated server in a different geographic location.
• Network Attached Storage (NAS) – Ideal for businesses with multiple websites. Configure RAID and remote sync.
• Specialized backup services – Tools like Backblaze, Wasabi, or Arq offer unlimited storage and version history.

Encrypt sensitive backups using tools like 7-Zip (AES-256), VeraCrypt, or GPG. Avoid storing passwords or API keys in plain text within backup files.

5. Test Your Backup Restoration

Many people assume their backups work—until they need them. The only way to confirm reliability is to test restoration.

Follow these steps:

1. Locate a recent backup file.
2. On a separate server, local machine, or staging environment, extract the backup.
3. Configure the web server (Apache/Nginx) to point to the restored files.
4. Check that all pages load correctly, images display, forms submit, and scripts execute.
5. Verify that configuration files (e.g., wp-config.php) have correct database credentials or are properly updated.
6. Test functionality: login, checkout, contact forms, plugins.

If anything fails, revisit your backup process. Did you miss a directory? Was a file corrupted during transfer? Document the issue and refine your method.

6. Maintain a Backup Log

Keep a simple text or spreadsheet log that records:

• Date and time of each backup
• Size of the backup file
• Location where it was stored
• Method used (FTP, script, control panel)
• Success/failure status
• Notes on any errors or anomalies

This log becomes invaluable during audits, migrations, or recovery scenarios. It also helps identify patterns—e.g., if backups consistently fail on weekends, you may need to adjust timing or server load.

Best Practices

Follow the 3-2-1 Backup Rule

This industry-standard principle ensures maximum resilience:

• 3 copies of your data: one primary and two backups.
• 2 different media types: e.g., local hard drive + cloud storage.
• 1 offsite copy: stored in a separate physical or geographic location.

Applying this rule minimizes risk from localized disasters like fire, theft, or ransomware.

Back Up Frequently

Frequency depends on how often your site changes:

• Static websites (HTML/CSS only): Weekly or monthly.
• Content-heavy blogs: Daily or after each major update.
• E-commerce sites: Multiple times daily, especially after product updates or orders.
• Dynamic applications: Hourly or real-time via replication.

Always back up immediately before performing major updates—CMS upgrades, plugin installations, theme changes, or server migrations.

Version Your Backups

Use clear, consistent naming conventions to distinguish between versions:

• website_2024-06-15_v1.tar.gz
• website_2024-06-16_v2.tar.gz
• website_prod_2024-06-15.zip

Include the date, environment (production/staging), and version number. Avoid generic names like “backup.zip” or “final.zip.”

Exclude Sensitive Data

Never back up files containing passwords, API keys, or private keys unless they are encrypted. Review your files for:

• .env files with database credentials
• ssh private keys
• config files with tokens

If you must include them, encrypt the entire backup archive with a strong password and store the password separately (e.g., in a password manager like Bitwarden or 1Password).

Monitor Backup Health

Set up alerts for failed backups. If you’re using scripts, add email notifications:

!/bin/bash
DATE=$(date +%Y-%m-%d)
SOURCE="/var/www/html"
DESTINATION="/home/user/backups/website_$DATE.tar.gz"
tar -czf "$DESTINATION" "$SOURCE" && echo "Backup successful" || echo "Backup failed" | mail -s "Website Backup Alert" admin@example.com

Use monitoring tools like UptimeRobot, Healthchecks.io, or custom scripts to ping a status endpoint after each backup completes.

Document Your Process

Create a simple README.md or internal wiki page detailing:

• Which files are backed up
• Where backups are stored
• How to restore them
• Who is responsible
• Frequency and schedule

This documentation ensures continuity if team members change or if you need to hand off maintenance.

Combine File Backups with Database Backups

While this guide focuses on files, remember that most dynamic websites (WordPress, Shopify, Magento) rely on databases to store content, users, and settings. A file backup alone won’t restore your blog posts, product listings, or user accounts.

Always pair file backups with regular database exports (e.g., using mysqldump for MySQL or pg_dump for PostgreSQL). Store both together and test restoration as a combined unit.

Tools and Resources

Free and Open-Source Tools

• FileZilla – Cross-platform FTP/SFTP client for manual file transfers.
• WinSCP – Windows-based SFTP and FTP client with scripting support.
• 7-Zip – Lightweight, open-source file archiver with AES-256 encryption.
• Rclone – Command-line tool to sync files to cloud storage (Google Drive, Dropbox, S3, etc.).
• rsync – Efficient file synchronization tool for Linux/macOS. Can be used to copy only changed files.
• tar and gzip – Native Unix utilities for compression and archiving.
• Healthchecks.io – Free service to monitor cron jobs and scripts. Sends alerts if a backup fails to run.

Commercial Backup Solutions

• BlogVault – WordPress-specific backup plugin with one-click restore, staging, and malware scanning.
• UpdraftPlus – Popular WordPress plugin offering scheduled backups to cloud storage.
• CodeGuard – Monitors and backs up files and databases, with real-time alerts and one-click restore.
• BackupBuddy – Comprehensive WordPress backup tool with migration features.
• Acronis Cyber Protect – Enterprise-grade backup and security suite for servers and websites.
• Backblaze B2 – Low-cost cloud storage ideal for large-scale website backups.

Cloud Storage Providers

• Google Drive – Free 15GB, affordable paid tiers, easy sharing.
• Dropbox – Excellent version history and collaboration features.
• Amazon S3 – Highly scalable, durable, and secure. Use with rclone or AWS CLI.
• Wasabi – S3-compatible, no egress fees, lower cost than AWS.
• Microsoft OneDrive – Integrated with Windows and Office 365.
• Backblaze Personal Backup – Unlimited storage for $7/month, simple interface.

Learning Resources

• Linux Command Line Basics – Learn shell scripting for automation.
• WordPress Backup Guide – Official documentation.
• Understanding SSL Certificates – Learn how to back up and renew certificates.
• How to Backup a Website with FileZilla – Video tutorial.
• Backup and Recovery (O’Reilly) – In-depth book on enterprise backup strategies.

Real Examples

Example 1: Small Business Blog (WordPress)

A local bakery runs a WordPress site with 200+ product images, 50 blog posts, and a contact form. The owner updates the site weekly with new menu items and seasonal promotions.

Backup Strategy:

• Daily automated backup using UpdraftPlus plugin.
• Backups stored on Google Drive and an external SSD.
• Backups include both files and database.
• Monthly test restoration on a local XAMPP server.

Outcome: After a plugin update broke the site, the owner restored from a 24-hour-old backup in under 10 minutes. No data was lost, and sales continued uninterrupted.

Example 2: E-commerce Store (Custom PHP)

An online retailer sells handmade jewelry using a custom PHP/MySQL platform. The site processes 50+ orders daily and has 1,200 product images.

Backup Strategy:

• Hourly rsync script copies /var/www/html to a remote backup server.
• Every 2 hours, MySQL database is dumped using mysqldump and stored separately.
• Backups are encrypted with GPG and uploaded to Wasabi S3.
• Weekly test restore on a staging server.
• Backup log maintained in a shared Notion dashboard.

Outcome: After a server crash caused by a DDoS attack, the team restored the entire site within 2 hours using the latest backup. Customer data and order history were preserved.

Example 3: Developer Portfolio (Static HTML)

A freelance developer maintains a static portfolio site hosted on GitHub Pages. The site has 15 HTML files, 3 CSS files, 10 JavaScript files, and 40 images.

Backup Strategy:

• Code is already version-controlled in a private GitHub repository.
• Additional backup created weekly using tar and uploaded to Dropbox.
• SSL certificate private key is stored in a password manager.

Outcome: When GitHub experienced an outage, the developer was able to redeploy the site from their local backup within minutes, maintaining client trust.

Example 4: Nonprofit Organization (Joomla)

A nonprofit runs a Joomla site with donor forms, event calendars, and volunteer signups. Volunteers manage content with limited technical skills.

Backup Strategy:

• Monthly full backup via cPanel, downloaded by the admin.
• After every content update, a manual backup is triggered and emailed to two staff members.
• Backups stored on a password-protected NAS device in the office.

Outcome: After a malicious plugin was installed, the site was compromised. The admin rolled back to the last clean backup, removed the plugin, and updated Joomla—avoiding data loss and reputational damage.

FAQs

How often should I backup my website files?

Frequency depends on how often your site changes. For static sites, weekly is sufficient. For blogs or CMS sites with daily updates, daily backups are recommended. E-commerce or high-traffic sites should back up multiple times per day.

Is backing up only the database enough?

No. The database stores content like posts and users, but not your theme files, plugins, images, or configuration files. A full backup requires both files and database.

Can I restore a website backup on a different server?

Yes, but you may need to adjust configuration files (e.g., database host, URL paths, file permissions). Always test restoration on a staging environment first.

What’s the difference between a full backup and an incremental backup?

A full backup copies all files every time. An incremental backup only copies files that have changed since the last backup. Incremental backups save space and time but require the full backup to restore completely.

Are website backups encrypted?

By default, most backups are not encrypted. Always encrypt sensitive backups using tools like 7-Zip, GPG, or VeraCrypt, especially if stored in the cloud.

How do I know if my backup is corrupted?

Test restoration regularly. If files fail to load, directories are missing, or scripts throw errors, the backup may be corrupted. Check file sizes and compare checksums (MD5/SHA256) if possible.

Can I use my web host’s backup service?

Yes, but don’t rely on it exclusively. Many hosts retain backups for only 7–14 days and may not include all files. Use their service as a secondary option, not your primary backup.

What should I do if I lose my website and have no backup?

Contact your hosting provider immediately—they may have a recent snapshot. If not, you may need to rebuild from scratch. Use tools like the Wayback Machine (archive.org) to recover archived versions of your pages. Prevention is always better than recovery.

Do I need to backup my SSL certificate?

Yes. SSL certificates and private keys are critical for secure connections. Losing them means you’ll need to reissue and reconfigure them, causing downtime. Back them up securely and store them separately from your website files.

What’s the easiest way to backup a WordPress site?

Use a plugin like UpdraftPlus or BlogVault. They automate file and database backups and allow one-click restores to cloud storage with minimal setup.

Conclusion

Backing up website files is not a one-time task—it’s an ongoing discipline that protects your digital assets, reputation, and livelihood. Whether you manage a simple static site or a complex e-commerce platform, the principles remain the same: identify what matters, back it up regularly, store it securely, and test restoration often.

The tools and methods outlined in this guide—from manual FTP transfers to automated scripts and cloud storage—are accessible to users of all skill levels. The key is consistency. Set up your system once, document it clearly, and review it quarterly. Don’t wait for disaster to strike before you act.

Remember: A backup that isn’t tested is not a backup. A file that isn’t stored offsite is at risk. And a website without a plan for recovery is a business waiting to fail.

Take control today. Implement one step from this guide—whether it’s scheduling your first automated backup or testing a restoration—and build from there. Your future self—and your visitors—will thank you.