While Cobalt nanoparticles (Co NPs) are useful for catalytic Oxone activation, it is more advantageous to embed/immobilize Co NPs on nitrogen-doped carbon substrates to provide synergy for enhancing catalytic performance. Herein, this study proposes to fabricate such a composite by utilizing covalent organic frameworks (COF) as a precursor. Through complexation of COF with Co, a stable product of Co-complexed COF (Co-COF) can be synthesized. This Co-COF is further converted through pyrolysis to N-doped carbon in which cobaltic NPs are embedded. Owing to its well-defined structures of Co-COF, the pyrolysis process transforms COF into N-doped carbon with a bubble-like morphology. Such Co NP-embedded N-doped carbon nanobubbles (CoCNB) with pores, magnetism and Co, shall be a promising catalyst. Thus, CoCNB shows a much stronger catalytic activity than commercial Co3O4 NPs to activate Oxone to degrade toxic Amaranth dye (AMD). CoCNB-activated Oxone also achieves a significantly lower Ea value of AMD degradation (i.e., 27.9 kJ/mol) than reported Ea values in previous literatures. Besides, CoCNB is still effective for complete elimination of AMD in the presence of high-concentration NaCl and surfactants, and CoCNB is also reusable over five consecutive cycles.