Advances in DNA sequencing technology provide the possibility to analyse and characterize the genetic material from microbial populations (the microbiome) as a whole. Such comprehensive analysis of a microbiome using these 'metagenomic' approaches offers the potential to understand industrial, clinical and environmental microbiology to a level of detail that is unfeasible using conventional molecular or culture-based methods. However, the complexity offered by metagenomic analysis is also the weakness of this method and poses considerable challenges during analytical standardisation. In this manuscript, we discuss options for developing control materials for metagenomic analysis and describe our preliminary work investigating how such materials can be used to assist metagenomic measurements. The control materials we have developed demonstrate that, when performing 16S rDNA sequencing, different library preparation methods (incorporating adapters before and after the PCR) and small primer mismatches can alter the reported metagenomic profile. These findings illustrate that metagenomic analysis can be heavily biased by the choice of method and underpin the need for control materials that can provide a useful tool in informing choice of protocol for accurate analysis.