Consumer goods contain multiwall carbon nanotubes (MWCNTs) that could be released during product life cycles into the environment, where their effects are uncertain. Here, we assessed MWCNT bioaccumulation in the protozoan Tetrahymena thermophila via trophic transfer from bacterial prey (Pseudomonas aeruginosa) versus direct uptake from growth media. The experiments were conducted using 14C-labeled MWCNT (14C-MWCNT) doses at or below 1 mg/L, which proved subtoxic since there were no adverse effects on the growth of the test organisms. A novel contribution of this study was the demonstration of the ability to quantify MWCNT bioaccumulation at low (sub μg/kg) concentrations accomplished by employing accelerator mass spectrometry (AMS). After the treatments with MWCNTs at nominal concentrations of 0.01 mg/L and 1 mg/L, P. aeruginosa adsorbed considerable amounts of MWCNTs: (0.18 ± 0.04) μg/mg and (21.9 ± 4.2) μg/mg bacterial dry mass, respectively. At the administered MWCNT dose of 0.3 mg/L, T. thermophila accumulated up to (0.86 ± 0.3) μg/mg and (3.4 ± 1.1) μg/mg dry mass by trophic transfer and direct uptake, respectively. Although MWCNTs did not biomagnify in the microbial food chain, MWCNTs bioaccumulated in the protozoan populations regardless of the feeding regime, which could make MWCNTs bioavailable for organisms at higher trophic levels.