MicroRNAs (miRNAs) are short endogenous molecules of RNA that influence cell regulation by suppressing genes. Their ubiquity throughout all branches of the tree of life has suggested their central role in many cellular functions. Nowadays, several personalized medicine applications rely on miRNAs as biomarkers for diagnoses, prognoses, and prediction of drug response. The increasing ease of sequencing miRNAs contrasts with the difficulty of accurately quantifying their concentration. The use of general purpose aligners is only a partial solution as they have limited possibilities to accurately solve ambiguous mapping due to the short length of these sequences. We developed E Z c o u n t, an all-in-one software that, with a single command, performs the entire quantification process: from raw fastq files to read counts. Experiments show that E Z c o u n t is more sensitive and accurate than methods based on sequence alignment, independently of the library preparation protocol and sequencing machine. The parallel architecture of E Z c o u n t makes it fast enough to process a sample in minutes using a standard workstation. E Z c o u n t runs on all of the most common operating systems (Linux, Windows and MacOS) and is freely available for download at https://gitlab.com/BioAlgo/miR-pipe . A detailed description of the datasets, the raw experimental results, and all the scripts used for testing are available as supplementary material. Display Omitted • EZcount searches miRNAs in the reads, instead of aligning reads to the reference. • EZcount resolves ambiguous alignments using quality scores. • EZcount outperforms the existing tools in terms of properly matched reads. • EZcount self-tune without the need to know the adapter sequence or other library parameters.