flowerMD is a package for reproducibly performing multi-stage HOOMD-blue (Anderson et al., 2020) simulation workflows. It enables the programmatic specification of tasks including definition of molecular structures, forcefield definition and application and chaining together simulation stages (e.g., shrinking, equilibration, simulating a sequence of ensembles, tensile testing, etc.) through an extensible set of Python classes. The modular design supports a library of workflows for organic macromolecular and polymer simulations. Tutorials are provided to demonstrate package features and flexibility.