The main disadvantage of green roofs is that the initial cost of installing a green roof can be double that of a normal roof. Depending on what kind of green roof it is, the maintenance costs could be higher, but some types of green roof have little or no ongoing cost. Some kinds of green roofs also place higher demands on the waterproofing system of the structure, both because water is retained on the roof and due to the possibility of roots penetrating the waterproof membrane. Another disadvantage is that the wildlife they attract may include pest insects which could easily infiltrate a residential building through open windows.
The additional mass of the soil substrate and retained water places a large strain on the structural support of a building.  This makes it unlikely for intensive green roofs to become widely implemented due to a lack of buildings that are able to support such a large amount of added weight as well as the added cost of reinforcing buildings to be able to support such weight. Some types of green roofs do have more demanding structural standards especially in seismic regions of the world.  Some existing buildings cannot be retrofitted with certain kinds of green roofs because of the weight load of the substrate and vegetation exceeds permitted static loading. The weight of a green roof caused the collapse of a large sports hall roof in Hong Kong in 2016. In the wake of the disaster numerous other green roofs around the territory were removed.
Green roofs require significantly more maintenance and maintenance energy compared to a standard roof. Standard maintenance include removing debris, controlling weeds, deadhead trimming, checking moisture levels, and fertilizing. The maintenance energy use for green roofs has many variables including: climate, intensity of rainfall, type of building, type of vegetation, and external coatings. The most significant effect comes from scarce rainfall which will increase the maintenance energy due to the watering required. During a 10-year roof maintenance cycle a house with a green roof requires more retrofit embodied energy than a house with a white roof. The individual components of a green roof have  implications during the manufacturing process have additional implications compared to a conventional roof. The embodied energy for green roof components are   of green roof. This value is equivalent to 6448 g C m which is significantly greater than 378 g C m Criteria for waste management practices when green roofs reach their end-of-life remain uncodified.
Both sod roofs and LWA-based (Lightweight Aggregates) roofs have been found to have a negative impact on the quality of their resulting runoff.