Qubits based on ions trapped in linear radio-frequency traps form a successful platform for quantum computing, due to their high fidelity of operations, all-to-all connectivity, and degree of local control. In principle, there is no fundamental limit to the number of ion-based qubits that can be confined in a single 1D register. However, in practice, there are two main issues associated with long trapped-ion crystals, that stem from the “softening” of their modes of motion, upon scaling up: high heating rates of the ions’ motion and a dense motional spectrum; both impede the performance of high-fidelity qubit operations. Here, we propose a holistic, scalable architecture for quantum computing with large ion crystals that overcomes these issues. Our method relies on dynamically operated optical potentials that instantaneously segment the ion crystal into cells of a manageable size. We show that these cells behave as nearly independent quantum registers, allowing for parallel entangling gates on all cells. The ability to reconfigure the optical potentials guarantees connectivity across the full ion crystal and also enables efficient midcircuit measurements. We study the implementation of large-scale parallel multiqubit entangling gates that operate simultaneously on all cells and present a protocol to compensate for crosstalk errors, enabling full-scale usage of an extensively large register. We illustrate that this architecture is advantageous both for fault-tolerant digital quantum computation and for analog quantum simulations. Published by the American Physical Society 2024