DOEE is organized into, and carries out its mission through, the following administrative divisions:
Operations Services Administration
- Support Services Division
- Information Technology Division
- Grants Management Division
Energy Administration
- Building Performance Division
- Clean Energy Division
- Energy Initiatives and Data Division
Environmental Services Administration
- Toxic Substances Division
- Air Quality Division
- Lead-Safe and Healthy Homes Division
- Rail Safety and Emergency Response Division
Natural Resources Administration
- Fisheries and Wildlife Division
- Inspection and Enforcement Division
- Regulatory Review Division
- Watershed Protection Division
- Water Quality Division
Urban Sustainability Administration
- Green Building and Climate Branch
- Sustainability and Equity Branch
Utility Affordability Administration
- Residential Services Division
- Utility Assistance Division