Recently, the development of flexible supercapacitors has received significant attention due to their application in flexible electronics such as bendable mobile phones, flexible displays and wearable devices. Owing to numerous advantages such as excellent mechanical strength, low cost, high porosity and natural abundance, bacterial nanocellulose (BNC) is considered to be highly attractive for the fabrication of flexible supercapacitors. This work demonstrates that BNC can serve as an ideal layered matrix for incorporation of active two-dimensional (2D) materials. A novel strategy for the incorporation of graphene oxide (GO) sheets into layered BNC during its growth is presented. GO flakes can be interlocked within the nanocellulose network during BNC growth, enabling facile chemical reduction of GO sheets, which prevents their restacking and loss of active area and leads to excellent energy storage performance as well as mechanical flexibility. Significantly, the fabrication approach demonstrated here can be extended to other 2D nanomaterials to realize flexible BNC-based energy storage devices.