How to Improve WordPress Security: 5 Proven Best Practices

Securing a WordPress site is no longer optional. With rising brute-force attacks, malware injections, and plugin vulnerabilities, applying proper WordPress security best practices is essential for agencies and site managers responsible for client infrastructure.

If you manage multiple websites, security is not a one-time task; it’s ongoing risk management. A hacked site rarely means just a quick fix. It often leads to emergency cleanup, client frustration, lost SEO rankings, and unplanned downtime. In most cases, the breach doesn’t start with WordPress core. It starts with outdated plugins, insecure themes, or weak server configuration.

In this guide, I’ll walk you through a structured approach to improving and securing your WordPress site. I’ll cover practical WordPress hardening steps and explain why combining application-level protection with WordPress server security creates a more stable and scalable defense.

The Reality of WordPress Security

WordPress security means protecting your website from unauthorized access, malware injection, brute-force attacks, and server-level vulnerabilities through proper updates, authentication, hardening, and infrastructure configuration.

According to security reports, the majority of WordPress vulnerabilities originate from outdated plugins and themes rather than WordPress core.

Most vulnerabilities originate from:

• Outdated plugins
• Poorly coded themes
• Abandoned extensions
• Weak authentication practices

If you manage 20 client websites, you are not maintaining one system. You are maintaining 20 separate plugin stacks, 20 update cycles, and 20 potential entry points.

Traditional security setups rely heavily on plugins. These plugins scan for malware, limit login attempts, and add firewall rules. But there is a structural limitation: they work only after WordPress loads.

That means:

• The request hits your server.
• PHP starts executing.
• WordPress initializes.

Then the plugin decides whether the request is malicious.

A better approach is to stop malicious traffic before WordPress even starts running. That is where server-level hardening becomes important.

1. Core Hardening: The Foundations You Cannot Skip

Before discussing advanced infrastructure security, you need to get the basics right.

Keep Everything Updated – But Do It Strategically

Updates remain one of the most important defenses. Many attacks target known vulnerabilities that already have patches available. However, manually logging into every site to check updates is inefficient and error-prone.

A centralized management system, like what FlyWP provides, allows you to:

• View updates across multiple sites from one dashboard
• Apply patches in bulk
• Reduce forgotten or delayed updates

For agencies, this turns updates from reactive work into a controlled process.

Strengthen Authentication

Weak login security is still one of the easiest ways for attackers gain access.

At a minimum, every site should:

• Enable Two-Factor Authentication (2FA)
• Avoid using “admin” as a username
• Use strong, unique passwords

Brute-force bots typically target /wp-admin and try common usernames. Removing predictable credentials immediately reduces exposure.

If you’re managing client access, avoid sharing passwords over email or chat. Temporary login systems or secure access links reduce credential leakage.

Fix File and Folder Permissions

File permissions are often overlooked but extremely important.
Standard secure configuration should be:

• Directories → 755
• Files → 644

Incorrect permissions may allow attackers to modify files or inject malicious scripts. If you provision servers manually, you need to pay attention. Modern server management platforms set secure defaults automatically, reducing configuration mistakes.

2. Move Security to the Server Level

When it comes to WordPress server security, relying only on plugins is often not enough. True WordPress hardening starts at the infrastructure level – before WordPress even loads.

If you are serious about protecting your WordPress site at scale, you must address infrastructure.

Isolate Sites from Each Other

Many agencies host multiple sites on the same VPS. If all sites share the same environment, a compromise in one site can affect others.

Container-based isolation solves this.

For example, FlyWP uses Docker containers to isolate each WordPress site. That means:

• Each site runs in its own container
• Separate file system
• Separate services

If Site A is infected, Site B remains untouched.

For agencies, this is not a luxury feature. It is risk containment.

Block Malicious Traffic Before WordPress Loads

Most popular security plugins, such as Wordfence, operate inside WordPress. They analyze traffic after PHP has started.

Server-level firewalls work differently.

With Nginx-level rules or 7G/8G firewall configurations:

• Suspicious patterns are blocked before PHP execution
• SQL injection attempts are filtered early
• Known malicious bots are rejected immediately
  

This reduces both risk and resource usage.

The practical benefit? Fewer server spikes during bot attacks and improved site performance.

Disable Unnecessary Entry Points

Some features in WordPress are rarely used but commonly targeted.

XML-RPC is one example. It enables remote publishing but is frequently abused for brute-force attacks.

Instead of installing another plugin to disable it, server-level toggles allow you to:

• Disable XML-RPC
• Restrict wp-admin access by IP
• Block direct access to sensitive files
  

Handling this at the server level keeps your WordPress stack lighter.

3. Secure the Database and File System

Beyond login and firewall protection, you must secure data storage and file execution paths.

Change the Default Database Prefix

Automated attacks often assume this naming convention. Changing the prefix during setup reduces predictable attack patterns.

It is not a complete solution on its own, but it removes low-effort automated targeting.

Protect Critical Directories

Directories such as:

• wp-content
• wp-includes

Should not allow arbitrary PHP execution, especially inside upload folders.

Server-level rules can:

• Prevent PHP execution inside /uploads
• Block direct access to configuration files
• Restrict sensitive paths

This prevents many common malware persistence techniques.

Reduce Password Exposure

Many breaches happen not because of weak servers, but because credentials are shared insecurely.

Magic login systems allow temporary access without sharing actual admin passwords. These links expire automatically and reduce the risk of credential reuse or leakage.

For agencies managing developers and clients, this simplifies secure collaboration.

4. Backups and Recovery: Your Safety Net

Even with strong security, incidents can happen. The real question is not “Can you prevent every hack?” It is “How fast can you recover?”

Store Backups Off-Site

Never store backups on the same server as the live site.

If the server is compromised or fails, your backups disappear too.

Use remote storage such as:

• AWS S3
• DigitalOcean Spaces
• Google Cloud Storage
  

Off-site backups ensure that server failure does not equal total data loss.

Test One-Click Restore

Backup is incomplete without fast restoration.

If restoration requires manual reinstallation, database imports, and configuration, recovery becomes slow and stressful.

One-click restore allows you to revert to a clean state quickly. For client-facing agencies, this can be the difference between a minor incident and a long-term reputation issue.

5. WordPress Security Best Practices: Performance Without Heavy Plugins

Over time, many WordPress sites slowly accumulate security plugins. It usually starts with a firewall plugin. Then comes a login limiter. Later, a malware scanner is added. Eventually, another plugin is installed just to disable XML-RPC.

Individually, each plugin seems reasonable. But collectively, they increase complexity.

Every security plugin adds overhead. It increases:

• PHP execution time
• Database queries
• Memory usage
  

Most of these tools operate inside WordPress. That means every request must load WordPress first, initialize plugins, connect to the database, and then evaluate whether the request is safe. Even legitimate traffic goes through this full process.

When you manage high-traffic sites or multiple client websites, this overhead becomes noticeable. More plugins mean more potential conflicts, more update checks, and more maintenance work.

If security is handled at the server level instead, many of these plugin responsibilities become unnecessary. Firewall filtering, XML-RPC blocking, bot protection, and access restrictions can be applied before WordPress loads at all.

The practical result is:

• A cleaner WordPress stack
• Fewer plugin conflicts
• Better performance under load
• Lower long-term maintenance overhead

Security does not have to reduce performance. In many cases, infrastructure-level protection improves it because malicious requests are stopped before they consume PHP or database resources.

Plugin-Based Security vs. Server-Level Security

Here’s a simplified comparison:

Feature	Plugin-Based Security	Server-Level Security (FlyWP)
Blocks bad bots	After WordPress loads	Before WordPress loads
Resource usage	Higher	Lower
Multi-site management	Per site	Centralized
Site isolation	No	Yes (Docker)
Performance impact	Moderate to high	Minimal

If you manage one personal blog, plugin-based security may be sufficient. If you manage client infrastructure, server-level protection scales better.

How FlyWP Secures Your WordPress Ecosystem?

FlyWP isn’t just another hosting dashboard; it’s a dedicated security layer for your servers. Instead of waiting for a plugin to catch a threat, FlyWP shifts your defense to the infrastructure layer, stopping attacks before they ever reach your WordPress files.

1. True Site Isolation (The Docker Advantage):  On most servers, a single “dirty” plugin on one site can infect every other site on that server. FlyWP eliminates this “neighbor risk” by using Docker containers. Each site lives in its own isolated environment with a separate file system. If one site is targeted, the others remain untouched and secure.
   
2. The 8G Firewall: Blocking Threats at the Gate: Most firewalls load after WordPress starts, consuming your CPU and RAM. FlyWP uses a server-level 8G Firewall (Nginx-based). It filters SQL injections, XSS attacks, and malicious bots at the server gate. This means malicious traffic is dropped before it can even touch your database.
   
3. Centralized Agency Control: If you manage 20 sites, you shouldn’t have to do the same task 20 times. FlyWP allows you to manage bulk updates, backups, and security headers for all your sites from a single, centralized dashboard.
   
4. Effortless Hardening (One-Click Security): Hardening a site usually requires manual coding or multiple plugins. FlyWP provides a Security Dashboard where you can toggle professional-grade settings in seconds:
   
   – Disable XML-RPC: Shut down the #1 door for brute-force attacks.
   – Protect Sensitive Directories: Shield your wp-config.php and wp-content folders from direct execution.
   – Magic Login: Access your admin dashboard securely without sharing or storing passwords.

Summing Up

WordPress security is not about installing more plugins. It is about structuring your environment correctly.

If you manage multiple sites and want to move from reactive security to infrastructure-level protection, testing a platform like FlyWP with its 14-day trial can help you evaluate how much operational risk you can remove.

Because protecting your WordPress site should be systematic, not dependent on remembering one more plugin update.

WordPress Security FAQ

Below are the most common questions about how to secure a WordPress site, including practical WordPress hardening strategies and server-level security considerations.