Sylo uses an open-source system named the Signal Protocol to encrypt your communications. This is a non-federated cryptographic protocol that can be used to provide end-to-end encryption for voice and video calls, and instant messaging conversations. The protocol was developed by Open Whisper Systems in 2013 and was first introduced in the open-source TextSecure app, which later became Signal.

The protocol combines the Double Ratchet algorithm, prekeys, and a triple Elliptic-curve Diffie–Hellman (3-DH) handshake, and uses Curve25519, AES-256, and HMAC-SHA256 as primitives.