Chemically cross-linked, wet-stable cellulose nanofibril (CNF) aerogel beads were fabricated using a novel procedure. The procedure facilitated controlled production of millimetre-sized CNF aerogel beads without freeze-drying or critical point drying, while still retaining a highly porous structure with low density. The aerogel beads were mechanically robust in the dry state, supporting loads of 1.3 N at 70% compression, even after being soaked in water and re-dried. Furthermore, they displayed both a good stability in water and a remarkably good shape recovery after wet compression. Owing to the stability in water, the entire surface of the highly porous aerogel beads could be successfully functionalized with polyelectrolytes and carboxyl-functionalized single-wall carbon nanotubes (CF-SWCNTs) using the Layer-by-Layer technique, introducing a significant electrical conductivity (1.6 mS/cm) to the aerogel beads. The functionalized, electrically conducting aerogel beads could carry as much as 2 kA/cm2 and act as electrodes in a supercapacitor displaying a stabilized charge storage capacity of 9.8 F/g after 50 charging–discharging cycles.