How to Encrypt NAS Files: Native Settings vs. Client-Side Security

Buying a Network Attached Storage (NAS) device and setting a login password gives many users a false sense of safety. You might assume your files are secure because you need a password to view them, but this is the “Illusion of Security.” Without proper encryption, pulling the physical drives out of the box allows anyone with a PC to read your data instantly.

The stakes are higher than ever. Ransomware attacks increased by 11% globally in 2024, and the average cost of a data breach has reached a staggering $4.88 million (IBM, 2024). For small businesses and freelancers, relying solely on a login screen is no longer enough.

This guide explores exactly how to encrypt NAS files to protect your digital life. We will walk through the native settings available on Synology and QNAP devices—often called “Server-Side” encryption—and explain why switching to Client-Side encryption is the only way to turn your NAS into a truly secure, ransomware-proof storage vault.

The Two Ways to Secure a NAS: Server-Side vs. Client-Side

Before diving into settings menus, it is critical to understand that not all encryption is created equal. When securing a NAS, you generally have two options: letting the NAS handle the security (Server-Side) or handling it yourself before the data leaves your computer (Client-Side).

1. Server-Side Encryption (Native)

This is the default option on devices like Synology and QNAP. You log into the dashboard and tell the NAS to encrypt a specific folder. Ideally, the NAS holds the key and scrambles the data.

Think of this like a delivery service’s lockbox. As one cybersecurity researcher notes, “Server-side encryption is the ‘delivery company’s lockbox’ approach. You send your data to the server, and they lock it. But they also have the key.” If the delivery company (your NAS operating system) gets compromised, or if someone steals the box with the key attached, the lock is useless.

2. Client-Side Encryption (Zero-Knowledge)

This is the gold standard for privacy, often called what is zero knowledge encryption. Here, you encrypt the files on your computer using software like sekura.app before you drag them to the NAS.

The NAS receives data that is already scrambled. It doesn’t have the key, and it doesn’t know what the files are. It acts as a “dumb” storage box. Even if hackers compromise the NAS firmware, they only see gibberish.

With over 40% of cyberattacks now specifically targeting SMBs (Agility Portal, 2025), relying on the device itself to protect your data is a risky gamble. We recommend Client-Side encryption for anyone storing sensitive financial records, patient data, or client footage.

Why Native NAS Encryption Often Fails

While native encryption tools on Synology and QNAP are better than nothing, they contain significant security gaps that most setup guides ignore. By understanding these vulnerabilities, you can make an informed decision about your data strategy.

The “Admin-Proof” Gap

Native encryption does not protect you from the platform administrator.

Consider Marcus Lin, a financial consultant. Marcus stores personal tax documents and side-project ledgers on a corporate NAS, relying on the “Encrypted Folder” setting. He assumes his privacy is guaranteed. However, because the encryption is managed by the NAS OS, the company’s IT administrator—who holds root access—can reset passwords or mount shared folders to audit content. Marcus’s financial data was never truly private from the platform owners.

If you are using a NAS in a shared environment, native encryption does not hide your data from the people who manage the box.

The Ransomware Vulnerability

One of the biggest misconceptions is that native encryption stops ransomware. It usually doesn’t.

Take the case of Sarah Jenkins, a freelance video editor using a QNAP device. She fell victim to a targeted campaign similar to DeadBolt. Sarah had strong passwords, but the ransomware exploited a vulnerability in the NAS firmware itself, bypassing her login entirely.

Because Sarah’s encrypted folders were “mounted” (unlocked) so she could edit footage, the file system was visible to the OS. The ransomware simply encrypted her already encrypted files, double-locking them. Sarah faced a $1,200 ransom demand. Statistics show that only 11.2% of victims who pay actually recover all their data (Cyberint, 2024), making this a catastrophic failure of platform-native security.

The “Auto-Mount” Trap

To make life easier, NAS operating systems allow you to “Auto-mount” encrypted folders on startup. This is a critical error.

Dr. Aris Thorne, a clinical psychologist, used a Synology NAS for patient notes. To avoid typing a password daily, he enabled the “Key Manager” to auto-mount his folders. When his office was burglarized and the NAS stolen, the thieves simply plugged it in at their location. Because the key was stored on the device to allow auto-mounting, the drive unlocked automatically.

As experts in sysadmin communities warn: “If you store the encryption key on the same physical device as the encrypted data, you have effectively taped the key to the lock.” For proper password hygiene for smbs, never use auto-mount features for sensitive data.

Method 1: Using Native Encryption (Synology & QNAP)

If you decide to use the built-in tools despite the risks, here is how to enable them. Note that this generally reduces read/write speeds, so you may notice sluggish performance when transferring large files.

For Synology Users (DSM)

1. Log in to your DSM dashboard.
2. Go to Control Panel > Shared Folder.
3. Click Create (or select an existing folder and click Edit).
4. In the Encryption tab, check Encrypt this shared folder.
5. Enter a strong encryption key. Do not check “Mount automatically on startup” if you want protection against physical theft.
6. The system will prompt you to download a .key file. Keep this safe; without it, you cannot recover data if you forget the password.

For QNAP Users (QTS)

1. Log in to QTS.
2. Go to Control Panel > System > Storage & Snapshots.
3. Click Create > New Volume.
4. During the setup wizard, look for the Encryption option.
5. Select Encryption and enter your password.
6. Finish the wizard to format the volume.

The Downside: Beyond the security risks mentioned earlier, native encryption suffers from Metadata Leaks. Even if the contents of a file are locked, the filenames are often visible to the operating system. A file named Client_List_Cancer_Patients.pdf exposes sensitive information even if the PDF itself cannot be opened.

Method 2: Client-Side Encryption with Sekura (Recommended)

To eliminate the risks of admin snooping, firmware ransomware, and metadata leaks, the best approach is to encrypt files on your computer before they touch the network. This ensures the NAS never sees your actual data.

Here is how to secure your files using sekura.app:

1. Install Sekura Download and install the Sekura desktop application on your PC or Mac.

2. Create a Vault on the NAS Map your NAS drive to your computer (e.g., as the Z: drive). Open Sekura and create a new Vault. When asked where to save it, select your mapped NAS drive. Name it something generic like Z:/Project_Backups.

3. Drag and Drop Files Open the Sekura interface and drag your files into the vault.

Why This is Superior

• Zero-Knowledge: Even if the NAS is stolen or the firmware is hacked, the attacker only sees a folder full of scrambled code. They cannot brute-force the NAS login because your files aren’t protected by the NAS login—they are protected by AES-256 encryption controlled by you.
• Metadata Protection: Sekura obfuscates filenames and directory structures. Client_List_Cancer_Patients.pdf becomes a meaningless string of characters like 8f7d9a2b4c.sek, completely hiding the nature of your data.
• Portability: This answers the common fear: “What if my NAS hardware dies?” With native encryption, recovering data from proprietary file systems can be a nightmare. With Sekura, you simply pull the drives, plug them into any computer, and open your Vault. The hardware doesn’t matter.

Comparison: Native vs. Sekura

Feature	Native NAS Encryption	Sekura (Client-Side)
Protection vs. Physical Theft	Low (If auto-mount is on)	High (Keys stay on your PC/Mind)
Protection vs. Admin Snooping	No (Admin has root access)	Yes (Zero-Knowledge)
Performance Impact	System-wide (Slows NAS CPU)	On-demand (Uses PC CPU)
Filename/Metadata Encryption	Rarely (Filenames often visible)	Yes (Full obfuscation)
Recovery if Device Fails	Difficult (Proprietary OS)	Easy (Universal access)

Frequently Asked Questions

Can ransomware encrypt files that are already encrypted by the NAS? Yes. If you have “mounted” (unlocked) your encrypted shared folder to work on files, the ransomware sees it as a valid file system. It will encrypt your data again, effectively locking you out of your own encrypted vault. Client-side encryption prevents this by ensuring the files look like gibberish to the ransomware in the first place.

What is the difference between volume encryption and shared folder encryption? Volume encryption locks the entire hard drive, while shared folder encryption locks specific directories. Volume encryption is generally more secure but makes data recovery much harder if the NAS hardware fails. Shared folder encryption is more flexible but susceptible to metadata leaks.

Why can’t I see thumbnails on my encrypted NAS folders? This is actually a good sign. If you use client-side encryption, the NAS operating system cannot read the file to generate a preview thumbnail. If you can see thumbnails of your “secure” photos on the NAS web dashboard, your encryption is not providing total privacy.

Is it better to encrypt files on my computer before uploading? Yes. This is the definition of client-side encryption. It ensures that your data is protected during transit (while moving over the network) and at rest (while sitting on the drive). For tips on sharing these secure files with colleagues, check our guide on how to share encrypted files.

Conclusion

Native encryption on Synology or QNAP devices is better than leaving your files completely exposed, but it requires you to trust the device, the firmware, and the administrator. In a world where ransomware attacks are becoming smarter and more frequent, that is a significant risk.

For sensitive data—whether it’s financial records, medical history, or creative IP—you should treat your NAS as an untrusted storage medium. By using sekura.app to encrypt your files locally, you ensure that no matter what happens to the physical box, your data remains yours alone.

Ready to secure your NAS? Download sekura.app today and create your first zero-knowledge vault.