We demonstrate a SWAP gate between laser-cooled ions in a segmented microtrap via fast physical swapping of the ion positions. This operation is used in conjunction with qubit initialization, manipulation and readout, and with other types of shuttling operations such as linear transport and crystal separation and merging. Combining these operations, we perform quantum process tomography of the SWAP gate, obtaining a mean process fidelity of 99.5(5)%. The swap operation is demonstrated with motional excitations below 0.05(1) quanta for all six collective modes of a two-ion crystal, for a process duration of 42 µs. Extending these techniques to three ions, we reverse the order of a three-ion crystal and reconstruct the truth table for this operation, resulting in a mean process fidelity of 99.96(13)% in the logical basis.The last decade has seen substantial progress towards scalable quantum computing with trapped ions. Gate fidelities reach fault-tolerance thresholds [1], and first steps towards realizing decoherence-free qubits have been demonstrated [2]. Moreover, microfabricated, segmented ion traps continue to mature as an experimental low-noise environment [3,4] hosting multi-qubit systems [5,6]. In the seminal proposal from Kielpinsky, Monroe and Wineland [7] for such quantum CCD chip, scalability is reached through ion shuttling operations, where trapped-ion qubits are moved between different trap sites through application of suitable voltage waveforms to the trap electrodes. Since the first demonstration of ion shuttling in segmented traps [8], the development of trap control hardware has progressed [9,10]. This has recently led to demonstrations of fast ion shuttling at low final motional excitation [11,12]. It is currently an open question if a trapped-ion quantum computer should be based on large processing units hosting thousands of qubits [13,14] or on a modular architecture of medium-sized nodes with photonic interconnectivity [15]. With current technology, the possibilities for high-fidelity coherent control and readout of ion strings consisting of more than a few ions are limited, such that ion shuttling is required in either case. For universal quantum computation, two-qubit gates need to be performed between arbitrary pairs of ions, such that reordering ion strings becomes a necessary. Furthermore, if multiple ion species [16] are employed for sympathetic cooling [17] or ancilla-based syndrome readout via inter-species entangling gates [18,19], deterministic ion reconfiguration is ultimately required.To that end, segmented ion traps bearing junctions with T[20], X [21,22] or Y[23] geometry have been developed and tested. Junctions increase the design complexity of the traps and allow only for sequential ion transport. Shuttling through junctions may yield large motional excitations, which precludes the execution of two-qubit gates. In this work, we perform ion reorder- ing via on-site swapping of ions through application of suitable electric potentials. , where an external magnetic field lifts t...