Next Generation Sequencing technologies have enabled many advances across biology with microbial ecology benefiting primarily through expanded sample sizes. Although the cost of running sequencing instruments has decreased substantially over time, the price of library preparation methods has largely remained unchanged. We developed a low cost, miniaturized (5 \u00b5L), high-throughput (384-sample), amplicon library preparation method with the acoustic liquid handler, Echo 550. Our method reduces costs of library preparation to $1.42 USD per sample, a 58% reduction compared to existing automated methods and a 21-fold reduction from commercial kits, without compromising sequencing success or distorting the microbial community composition analysis. The cost savings of implementing the miniaturized library preparation (going from triplicate 25 \u00b5L reactions to triplicate 5 \u00b5L reactions) are large enough to cover a MiSeq sequencing run for 768 samples, while preserving accurate microbiome measurements.