Abstract Motivation Bisulfite sequencing (BSseq) processing is among the most cumbersome next generation sequencing (NGS) applications. Though some BSseq processing tools are available, they are scattered, require puzzling parameters and are running-time and memory-usage demanding. Results We developed P3BSseq, a parallel processing pipeline for fast, accurate and automatic analysis of BSseq reads that trims, aligns, annotates, records the intermediate results, performs bisulfite conversion quality assessment, generates BED methylome and report files following the NIH standards. P3BSseq outperforms the known BSseq mappers regarding running time, computer hardware requirements (processing power and memory use) and is optimized to process the upcoming, extended BSseq reads. We optimized the P3BSseq parameters for directional and non-directional libraries, and for single-end and paired-end reads of Whole Genome and Reduced Representation BSseq. P3BSseq is a user-friendly streamlined solution for BSseq upstream analysis, requiring only basic computer and NGS knowledge. Availability and Implementation P3BSseq binaries and documentation are available at: http://sourceforge.net/p/p3bsseq/wiki/Home/ Supplementary information Supplementary data are available at Bioinformatics online.