Currently, most carbon aerogels are based on carbon nanotubes (CNTs) or graphene, which are produced through a catalyst-assisted chemical vapor deposition method. Biomass based organic aerogels and carbon aerogels, featuring low cost, high scalability, and small environmental footprint, represent an important new research direction in (carbon) aerogel development. Cellulose and lignin are the two most abundant natural polymers in the world, and the aerogels based on them are very promising. Classic silicon aerogels and available organic resorcinol-formaldehyde (RF) or lignin-resorcinol-formaldehyde (LRF) aerogels are brittle and fragile; toughening of the aerogels is highly desired to expand their applications. This study reports the first attempt to toughen the intrinsically brittle LRF aerogel and carbon aerogel using bacterial cellulose. The facile process is catalyst-free and cost-effective. The toughened carbon aerogels, consisting of blackberry-like, core-shell structured, and highly graphitized carbon nanofibers, are able to undergo at least 20% reversible compressive deformation. Due to their unique nanostructure and large mesopore population, the carbon materials exhibit an areal capacitance higher than most of the reported values in the literature. This property makes them suitable candidates for flexible solid-state energy storage devices. Besides energy storage, the conductive interconnected nanoporous structure can also find applications in oil/water separation, catalyst supports, sensors, and so forth.