Many quantum computing platforms are based on a fundamentally two-dimensional physical layout. However, there are advantages (for example in fault-tolerant systems) to having a 3D architecture. Here we explore a concept called looped pipelines which permits one to obtain many of the advantages of a 3D lattice while operating a strictly 2D device. The concept leverages qubit shuttling, a well-established feature in platforms like semiconductor spin qubits and trappedion qubits. The looped pipeline architecture has similar hardware requirements to other shuttling approaches, but can process a stack of qubit arrays instead of just one. Simple patterns of intra-and inter-loop interactions allow one to embody diverse schemes from NISQ-era error mitigation through to fault-tolerant codes. For the former, protocols involving multiple states can be implemented with a similar space-time resource as preparing one noisy copy. For the latter, one can realise a far broader variety of code structures; in particular, we consider a stack of 2D codes within which transversal CNOTs are available. We find that this can achieve a cost saving of up to a factor of ∼ 80 in the space-time overhead for magic state distillation (and a factor of ∼ 200 with modest additional hardware). Using numerical modelling and experimentally-motivated noise models we verify that the looped pipeline approach provides these benefits without significant reduction in the code's threshold.