Preparation of high-quality sequencing libraries is a costly and time-consuming component of metagenomic next generation sequencing (mNGS). While the overall cost of sequencing has dropped significantly over recent years, the reagents needed to prepare sequencing samples are likely to become the dominant expense in the process. Furthermore, libraries prepared by hand are subject to human variability and needless waste due to limitations of manual pipetting volumes. Reduction of reaction volumes, combined with sub-microliter automated dispensing of reagents without consumable pipette tips, has the potential to provide significant advantages. Here, we describe the integration of several instruments, including the Labcyte Echo 525 acoustic liquid handler and the iSeq and NovaSeq Illumina sequencing platforms, to miniaturize and automate mNGS library preparation, significantly reducing the cost and the time required to prepare samples. Through the use of External RNA Controls Consortium (ERCC) spike-in RNAs, we demonstrated the fidelity of the miniaturized preparation to be equivalent to full volume reactions. Furthermore, detection of viral and microbial species from cell culture and patient samples was also maintained in the miniaturized libraries. For 384-well mNGS library preparations, we achieved a savings of over 80% in materials and reagents alone, and reduced preparation time by 90% compared to manual approaches, without compromising quality or representation within the library.After library preparation, the next step before putting samples on the sequencer is to pool samples to be able to multiplex sequencing. Final concentrations of each sample will vary from sample to sample depending on various things like RNA input, library prep, and PCR cycles among other factors. It is difficult to\u00a0manually quantify and pool uniformly 384 samples, so that is why we employ robots. To quickly and accurately pool hundreds of samples at a time, we employed a two-step method.\u00a0 Using the Labcyte Echo, equal volumes of each library are pooled together and sequenced on the Illumina iSeq or MiSeq sequencing platforms to determine the representation of each library in the total pool.\u00a0\u00a0Using this information, libraries were pooled using the Echo into a normalized pool for downstream sequencing on the Illumina NovaSeq.