The plant sRNA portal is an online resource integrating a workflow for identifying, predicting and annotating plant small RNAs (sRNA), and a database to store sRNA datasets with standardized metadata. The workflow (miRPursuit) is based on publicly available tools and allows the automated sequential application of data processing modules for analysis of sRNA datasets, including data preprocessing, filtering, annotation and reporting output. Additionally, tools for downstream analysis, such as expression matrix and prediction of sRNA target genes are integrated in the workflow. The database will work as a repository of the miRPursuit annotated sRNAs and other publicly available sRNAs, focusing mainly on woody plant data.