Initially focused on extract, transform, and load (ETL) processes and data analytics, the software has evolved to offer broader capabilities in various scientific and industrial applications.

The software allows users to create workflows by dragging and dropping functional components that automate data analysis tasks, integrate with databases, and perform various scientific computations.

The product supports multiple programming languages, including Python, .NET, Matlab, Perl, SQL, Java, VBScript, and R, giving users flexibility in integrating custom code into their workflows.

Additionally, Pipeline Pilot offers support for PilotScript, its own scripting language based on PLSQL, which allows users to perform custom data manipulations within their workflows.

Pipeline Pilot has continued to expand its capabilities with additional modules and toolsets for specific scientific tasks, such as next-generation sequencing analysis, cheminformatics, and polymer property prediction.

The interface, known as the Pipeline Pilot Professional Client, allows users to create workflows by selecting and arranging individual data processing units called "components."

Pipeline Pilot offers several add-ons called "collections," which are groups of specialized functions aimed at specific domains, such as genetic information processing or polymer analysis.