I’ve already written a post on the topic of mobile apps vs. web apps, which is based on the following core idea: it usually doesn’t make sense to use native apps (i.e., those developed specifically for your mobile operating system) and instead prefer web apps. Native apps often have deeper access rights to your device and can more easily extract (personal) data via interfaces – such as location, contacts, or usage behavior. Web apps, which you use in the browser, are generally much more limited in this respect and are therefore often more privacy-friendly. So if you’re serious about digital self-defense, you’re usually safer with web apps in everyday life: App vs. Web: Why It Matters How You Use Digital Services
Messaging Apps: An Exception to the Rule
However, when it comes to messaging services – especially those that offer end-to-end encryption (E2EE) – I have to re-qualify my general statement.
In this particular area, it makes more sense to prefer the native app. The reason: E2EE can be implemented in a much more robust way in native apps than in web applications.
What is End-to-End Encryption (E2EE)?
First, let’s clarify what end-to-end encryption (E2EE) actually means. E2EE ensures that only the sender and the intended recipient can read a message. No third party — not the messaging service, internet provider, or any potential attacker — can access the content. The message is encrypted on the sender’s device, transmitted in its encrypted form, and only decrypted on the recipient’s device. This differs from regular transport layer encryption (like HTTPS), where data is encrypted in transit but may be decrypted on the service provider’s servers. With E2EE, even if someone intercepts the data, the content remains unreadable.
Why is End-to-End Encryption (E2EE) harder to implement in web applications than in native apps?
Implementing E2EE in web applications is significantly more complex than in native applications. There are several technical and security-related reasons for this. The central challenges involve the integrity of the source code, the secure handling of cryptographic keys, and session management in the browser.
1. Code Integrity and Control
With native apps, the code is compiled once, signed, and installed on the device. The executable code remains the same each time it is used and can be verified for integrity via signatures. Not so with web applications: in this case, the JavaScript code is reloaded from the server each time the page is accessed.
This means: if the server is compromised or an attacker manages to position themselves as a man-in-the-middle between the user and the server, they could inject manipulated code – for example, with hidden backdoors or functions to intercept keys. This dynamic makes it difficult to ensure that the code executed in the browser is actually trustworthy.
2. Secure Access to Cryptographic Keys
Native apps use special, secure storage areas provided by the operating system to store private keys:
- iOS: Secure Enclave / Keychain
- Android: Keystore
These protected environments offer strong safeguards against unauthorized access, even if the app itself is compromised. Web applications, on the other hand, usually only have access to data stored locally in the browser. These storage locations are significantly more vulnerable to attacks – especially through cross-site scripting (XSS).
Additionally, although access to modern web APIs for secure key storage (e.g., Web Crypto API) is possible, in practice it’s often limited and difficult to implement securely – especially in a heterogeneous browser environment.
3. Session Handling
Managing sessions is particularly challenging for end-to-end encryption (E2EE) in web applications. Unlike native apps, which often stay logged in and run background processes continuously, web browser sessions are much more dependent on user actions. For example, simply closing a tab, updating the browser, or switching devices can lead to problems like:
- Temporary keys being lost
- Sessions becoming invalid
- Users needing to log in again, without a secure way to restore their encryption key
For E2EE to work properly, the encryption key must be both securely stored and reliably accessible. That’s a tough balance to strike in a web environment. Keys can’t be left in plain text, but they also need to be available when the session resumes. This creates a constant tension between keeping things secure and making them easy to use.
E2EE does not equal Privacy
Even if your messenger offers E2EE, that doesn’t automatically mean it doesn’t collect data about you. While the content of your messages may be encrypted, metadata is still generated. Metadata – such as who communicated with whom and when – is necessary to deliver messages. Some messaging services, especially WhatsApp, collect this information and use it for profiling purposes – despite E2EE.
If real privacy matters to you, you should rely on open messengers like Signal or well-implemented alternatives like Threema.
If you’re interested in a comparison of different services: the current issue of c’t magazine provides an excellent overview of which messenger is suitable for which use case:
https://www.heise.de/select/ct/2025/9/2505715264990543311
Conclusion
In everyday life, it often makes sense to prefer web apps – especially from a privacy perspective.
However, for messaging services, the rule is: if you want real end-to-end encryption, using the native app is usually the way to go.
The technical advantages in security and key management outweigh the otherwise critical privacy disadvantages of native applications – provided you use a trustworthy service.
Checklist
- Web apps are often the more privacy-friendly choice for everyday use.
- Native messenger apps, however, offer technically better conditions for real end-to-end encryption (E2EE).
- E2EE is difficult to implement securely in web applications – due to dynamic code and weaker key management, among other things.
- E2EE protects content, but not metadata – choose messengers that aim to protect both as much as possible.