A new encryption algorithm is proposed and designed which is followed by a verification algorithm used to access such Internet-of-Things (IoT) based systems. A three Layer Encryption Algorithm (3LEA) is designed to generate a cryptographic Quick Response (QR) tag. In order to use this QR-tag as a secret key with IoT-based systems, a three Processes Verification Algorithm (3PVA) has been proposed to verify QR-tag values. In order to make a decision either to approve or disapprove a request to access an IoT-based system, a three-Layer Protection Algorithm (3LPA) is proposed. 3LPVA applies math operations to authenticate confidentiality, integrity, and availability of QR-tag (i.e., smart key). Thus, once the smart key is verified, an access to the IoT-based system is allowed. The 3LEA, 3PVA, and 3LPA are designed in such a way and capsulated using a new Encryption Scheme Method (ESM). The ESM contributes much to IoT technology era in terms of systems security; it is used as a smart key designer and verifier for IoT access systems. The ESM is evaluated in terms of security factors, decryption time, robustness, unpredictability, and 3LEA’s technical evaluation. Results show good performance of robustness and an unpredictability behavior of 3LEA.