Embodiments of a method and system for improved microbiome sequencing can include: generating guide RNA complexes for a set of targets corresponding to a set of taxa associated with the microorganism-related condition; processing the biological sample with the gRNA complexes to generate microorganism nucleic acid fragments comprising a set of end regions associated with the set of targets; ligating the set of end regions with a set of adapters sharing an adapter sequence; and amplifying the set of targets based on the ligated set of end regions and a set of primers sharing a primer sequence associated with the adapter sequence.