Docking windows are special windows that can be arranged in various ways, in order to make the application more convenient to use. Docking windows are shown or hidden using the View/Docking Windows submenu. Many of Polymeter's features are accessed via docking windows.
| Standard | The toolbar, containing buttons for frequently used commands |
| Channels | Lets you edit the properties of each MIDI channel |
| Graph | Displays graphs of modulations |
| MIDI Input | Displays input MIDI events in real time |
| MIDI Output | Displays output MIDI events in real time |
| Mapping | Lets you edit translations and mappings of input MIDI events |
| Modulations | Lets you edit modulations for the selected tracks |
| Parts | Lets you edit the list of parts |
| Phase | Displays phase relationships for the selected tracks |
| Piano | Displays output notes in real time on a virtual piano keyboard |
| Presets | Lets you edit the list of presets |
| Properties | Lets you edit the master properties |
| Step Values | Lets you edit track step values numerically, using a grid view |