Mu-DNA is designed to be a simple and modular spin column-based DNA extraction ‘toolkit’ for the isolation of high purity DNA from multiple sample types. Here we present optimised Mu-DNA protocols for soil, tissue and water samples. Each protocol consists of five stages for DNA extraction: lysis, inhibitor removal, silica binding, wash and elution. Mu-DNA: Tissue has no inhibitor removal stage. All stages are designed to be modular and interchangeable between protocols. For example, an inhibitor removal stage can be added to a tissue protocol or a tissue protocol wash stage added to a soil protocol. The modular aspect allows for the creation of an optimised, bespoke DNA extraction for a specific sample type.