This study investigated simultaneous heavy metals removal and anthracene biodegradation by Rhodococcus opacus at different initial anthracene concentrations in the range 50–200 mg L−1. The heavy metals tested were Fe(III), Cu(II), Zn(II), Cd(II), Ni(II), and Pb(II) at 10 mg L−1 initial concentration: The organism was found to be well capable of removing the heavy metals along with high anthracene biodegradation efficiency. However, anthracene biodegradation rate by the organism was reduced due to these heavy metals. In addition, the heavy metals effect on R. opacus biomass growth followed the order: Cd > Ni > Pb > Cu > Zn > Fe. The total time to anthracene biodegradation increased from 144 to 216 h in the presence of Fe, Zn, Cu, or Pb, and it was up to 240 h in the presence of Cd or Ni. Compared with 70.2% (w/w) lipid accumulation by the bacterium in the absence of these heavy metals, a significant decline in the same was observed in the presence of the different heavy metals. These values were 41.2, 44.1, 52.1, 54.1, 58.6, and 63.1% (w/w) for Cd, Ni, Pb, Cu, Zn, and Fe, respectively. Field emission scanning electron microscopy integrated with energy dispersive X-ray spectroscopy and transmission electron microscopy of the biomass grown in the presence and absence of these heavy metals further confirmed a change in morphology of the bacterium due to the heavy metals. Fourier transmission infrared spectroscopy spectra of the biomass obtained during its growth in the presence and absence of the heavy metals confirmed the involvement of N–H, C–H bend, –CH2–(C=O), C–N stretch, C–H and O–H bending, and –C–Cl groups on the biomass for heavy metal uptake by the bacterium.