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In the scale-up of quantum computers, the framework underpinning fault-tolerance generally relies on the strong assumption that environmental noise affecting qubit logic is uncorrelated (Markovian). However, as physical devices progress well into the complex multi-qubit regime, attention is turning to understanding the appearance and mitigation of correlated -- or non-Markovian -- noise, which poses a serious challenge to the progression of quantum technology. This error type has previously remained elusive to characterisation techniques. Here, we develop a framework for characterising non-Markovian dynamics in quantum systems and experimentally test it on multi-qubit superconducting quantum devices. Where noisy processes cannot be accounted for using standard Markovian techniques, our reconstruction predicts the behaviour of the devices with an infidelity of $10^{-3}$. Our results show this characterisation technique leads to superior quantum control and extension of coherence time by effective decoupling from the non-Markovian environment. This framework, validated by our results, is applicable to any controlled quantum device and offers a significant step towards optimal device operation and noise reduction.