How Encrypted Messaging Apps Work: Matrix, Signal, and WhatsApp Compared

Introduction

In an age dominated by digital communication, the importance of privacy of information and secure messaging has never been greater. Whether it’s journalists protecting sources, companies safeguarding intellectual property, or everyday users trying to keep their conversations private, secure messaging apps play a crucial role in modern communication. Among the many options available, Signal, WhatsApp, and Telegram have come out as three of the most widely used messaging platforms that promise some level of end-to-end encryption (E2EE).

But not all encryption is created equal. While all three apps advertise security and privacy, their actual implementations of encryption protocols and security practices vary significantly. Signal is widely praised for its robust open-source protocol and prioritizing privacy in their work. WhatsApp uses a variant of the Signal Protocol, but is operated by Meta; a company whose business model depends on user data. Telegram, on the other hand, offers E2EE only in its "Secret Chats" and relies on its own homegrown MTProto protocol, which has faced criticism from security researchers.

This blog post provides a technical comparison of these three messaging platforms, focusing on their encryption methods, protocol designs, feature sets, and known vulnerabilities, all in the context of cryptographic safety and proper implementation. The goal is to help readers understand how these apps work under the hood; and make informed decisions about which platform best meets their security needs.

TL;DR – Secure Messaging at a Glance

• Signal: Top-tier security. End-to-end encrypted by default, zero metadata, open-source, built on rigorous cryptographic protocols.
• WhatsApp: Strong encryption, but trust depends on Meta. Backups, metadata collection, and sync features introduce risks.
• Telegram: Encryption is optional (Secret Chats only). Cloud-based chats are not end-to-end encrypted. Uses a custom, closed protocol.

Bottom Line: For high-security needs, choose Signal. WhatsApp is decent with caveats. Telegram trades off privacy for convenience.

What is End-to-End Encryption?

At the heart of secure messaging apps lies a powerful privacy-preserving technology: end-to-end encryption (E2EE). Unlike traditional encryption approaches that protect data only during transmission or while stored on a server, E2EE ensures that only the sender and the intended recipient can decrypt a message. Not even the service provider, nor any intermediary server, can access the content of the communication.

In a properly implemented E2EE system, encryption and decryption occur exclusively on the devices involved. Messages are encrypted before they leave the sender’s device and decrypted only upon arrival at the recipient’s. Even if a malicious actor intercepts the data mid-transit or gains access to the service’s servers, the content remains encrypted without the recipient’s private key.

This contrasts with two older security models:

• Encryption in Transit: protects data while it's being transferred between devices and servers. However, the data is usually decrypted on the server side before being forwarded.
• Encryption at Rest: protects stored data (e.g., backups, databases), but if the server is compromised, decrypted data may still be accessible.

E2EE offers significantly better protection against mass surveillance, man-in-the-middle attacks, and rogue server operators. However, it also limits functionality like cloud-based backups, full-text search, and seamless multi-device syncing; unless special care is taken to preserve encryption during those processes.

All three apps, Signal, WhatsApp, and Telegram, claim to support E2EE. However, as we'll see, their protocols, defaults, and implementations differ substantially, resulting in different levels of real world security.

Protocol and Cryptographic Architecture

Signal: The Gold Standard in Secure Messaging

Signal is widely regarded as the benchmark for private communication. Its Signal Protocol is open-source, peer-reviewed, and now underpins WhatsApp, Facebook Messenger’s “Secret Conversations,” and Google’s RCS. The protocol achieves end-to-end encryption, forward secrecy, post-compromise security, and deniability through three tightly integrated building blocks:

1. X3DH (Extended Triple Diffie-Hellman) – one-shot session setup
2. Pre-keys – enable asynchronous messaging
3. Double Ratchet – provides a new encryption key for every message

Initial Key Agreement: X3DH

When Alice starts a chat with Bob, she fetches Bob’s pre-key bundle and computes four elliptic-curve DH values:

DH₁ = DH(IK_A, SPK_B)
DH₂ = DH(EK_A, IK_B)
DH₃ = DH(EK_A, SPK_B)
DH₄ = DH(EK_A, OPK_B)

The secrets feed an HKDF to derive the session root key:

SK = HKDF(DH₁ || DH₂ || DH₃ || DH₄, info)

Ongoing Messaging: The Double Ratchet

Every message advances two ratchets, ensuring forward secrecy and post-compromise security.

Kₙ₊₁ = HMAC-SHA256(Kₙ, "message key")

Cryptographic Primitives

Security Features

• Forward secrecy
• Post-compromise security
• Deniability
• Minimal metadata

Practical Trade-Offs

• Limited multi-device sync
• No cloud backups by default
• Physical device compromise risk (common to all apps)

WhatsApp: Widespread Encryption with Centralized Trust

WhatsApp uses the Signal Protocol for E2EE, but Meta’s infrastructure introduces additional trust considerations.

Encryption Protocol

• Uses X3DH and Double Ratchet
• Uses Curve25519, AES-256-GCM, HMAC-SHA-256
• Transports messages via XMPP over TLS

Backups and Multi-Device Behavior

• Cloud backups not E2EE by default
• Optional encrypted backups via password/HSM vault
• Multi-device sync increases attack surface

WhatsApp Cryptographic Stack

WhatsApp Security Considerations

• Metadata collection
• Backups weaken guarantees
• Server-side message queuing

Telegram: Encryption on Demand, Cloud by Default

Telegram promotes itself as secure, but only Secret Chats use E2EE. Regular chats are cloud-based and not end-to-end encrypted.

Encryption Model: MTProto 2.0

• Cloud Chats: encrypted client–server, not E2EE
• Secret Chats: fully E2EE, no cloud sync

MTProto Technical Structure

• AES-256-IGE encryption (no built-in authentication)
• Message key derived from SHA1
• DH exchange with server for key establishment

Key Storage & Trust Model

• Telegram stores decryption keys for cloud chats
• Secret Chats do not sync across devices
• No independent audits

MTProto vs. Signal

Telegram Vulnerabilities

Conclusion

End-to-end encryption is essential for private communication, but implementations vary widely.

• Signal: the most secure, with rigorous cryptographic foundations and minimal metadata.
• WhatsApp: strong encryption, but weakened by metadata collection, cloud backups, and centralization under Meta.
• Telegram: only optional E2EE; cloud chats rely on a closed, less rigorous protocol.

Ultimately, Signal remains the top choice for high-security needs, while WhatsApp and Telegram involve trade-offs between usability and privacy.

No matter the choice, understanding how these protocols work, not just that they exist, is essential for making informed, secure decisions in an increasingly surveilled world.