Abstract Quantum key distribution (QKD) has established itself as a groundbreaking technology, showcasing inherent security features that are fundamentally proven. Qubit-based QKD protocols that rely on binary encoding encounter an inherent constraint related to the secret key capacity. This limitation restricts the maximum secret key capacity to one bit per photon. On the other hand, qudit-based QKD protocols have their advantages in scenarios where photons are scarce and noise is present, as they enable the transmission of more than one secret bit per photon. While proof-of-principle entangled-based qudit QKD systems have been successfully demonstrated over the years, the current limitation lies in the maximum distribution distance, which remains at 20 km fiber distance. Moreover, in these entangled high-dimensional QKD systems, the witness and distribution of quantum steering have not been shown before. Here we present a high-dimensional time-bin QKD protocol based on energy-time entanglement that generates a secure finite-length key capacity of 2.39 bit/coincidences and secure cryptographic finite-length keys at 0.24 Mbits s⁻¹ in a 50 km optical fiber link. Our system is built entirely using readily available commercial off-the-shelf components, and secured by nonlocal dispersion cancellation technique against collective Gaussian attacks. Furthermore, we set new records for witnessing both energy-time entanglement and quantum steering over different fiber distances. When operating with a quantum channel loss of 39 dB, our system retains its inherent characteristic of utilizing large-alphabet. This enables us to achieve a secure key rate of 0.30 kbits s⁻¹ and a secure key capacity of 1.10 bit/coincidences, considering finite-key effects. Our experimental results closely match the theoretical upper bound limit of secure cryptographic keys in high-dimensional time-bin QKD protocols (Mower et al 2013 Phys. Rev. A 87 062322; Zhang et al 2014 Phys. Rev. Lett. 112 120506), and outperform recent state-of-the-art qubit-based QKD protocols in terms of secure key throughput using commercial single-photon detectors (Wengerowsky et al 2019 Proc. Natl Acad. Sci. 116 6684; Wengerowsky et al 2020 npj Quantum Inf. 6 5; Zhang et al 2014 Phys. Rev. Lett. 112 120506; Zhang et al 2019 Nat. Photon. 13 839; Liu et al 2019 Phys. Rev. Lett. 122 160501; Zhang et al 2020 Phys. Rev. Lett. 125 010502; Wei et al 2020 Phys. Rev. X 10 031030). The simple and robust entanglement-based high-dimensional time-bin protocol presented here provides potential for practical long-distance quantum steering and QKD with multiple secure bits-per-coincidence, and higher secure cryptographic keys compared to mature qubit-based QKD protocols.