Adsorption-synergic biodegradation of a model PAH (phenanthrene, Phe) on MWCNT buckypaper surface with a potential PAH biodegrading bacterial strain Bacillus thuringiensis AT.ISM.11 has been studied in aqueous medium. Adsorption of Phe on buckypaper follows Dubinin-Ashtakhov model (R2 = 0.9895). MWCNT generally exerts toxicity to microbes but adsorbed layer of Phe prevents the direct contact between MWCNT and bacterial cell wall. FESEM study suggests that formation of biofilms occurred on buckypaper. Lower layer cells are disrupted and flattened as they are in direct contact with MWCNT but the upper layer cells of the developed biofilm are fully intact and functional. Force-distance curves of Bacillus thuringiensis AT.ISM.11 with buckypaper indicates adhesion forces varied from −10.3 to −15.6 nN with increasing contact time, which supports the phenomenon of biofilm formation. AFM surface statistical data of buckypaper suggests increase in bacterial cell count increases the Rms roughness (95.7242–632.565) while adhering to the buckypaper surface to form biofilm. We observed an enhanced Phe biodegradation of 93.81% from that of the 65.71% in 15 days’ study period, using buckypaper as a bio-carrier or a matrix for the microbial growth. GC-MS study identified phthalic acid ester as metabolite, which is the evidence of protocatechuate pathway degradation of Phe. Current study enlightens the interaction between hydrocarbons and microbes in presence of MWCNT buckypaper matrix in aqueous system for the first time. An enhancement in biodegradation of Phe by 28.10% has also been reported which can be a basis for CNT aided enhanced biodegradation studies in future.