Microorganisms forming a biofilm might become multidrug-resistant by information exchange. Multi-resistant, biofilm-producing microorganisms are responsible for a major portion of hospital-acquired infections. Additionally, these microorganisms cause considerable damage in the industrial sector. Here, we screened several nanoparticles of transition metals for their antibacterial properties. The nanoparticles sizes of nickel (<300 nm) and nickel oxide (<50 nm) were analyzed with transmission electron microscopy. We could show that the antibacterial efficacy of nickel and nickel oxide nanoparticles on Pseudomonas aeruginosa isolated from household appliances and Staphylococcus aureus was the highest. Interestingly, only P. aeruginosa was able to survive at high concentrations (up to 50 mM) due to clustering toxic nanoparticles out of the medium by biofilm formation. This clustering served to make the medium nearly free of nanoparticles, allowing the bacteria to continue living without contact to the stressor. We observed these clusters by CLSM, SEM, and light microscopy. Moreover, we calculated the volume of NiO particles in the bacterial biofilms based on an estimated thickness of 5 nm from the TEM images as an average volume of 3.5 × 10−6 µm3. These results give us a new perspective on bacterial defense mechanisms and might be useful in industries such as water purification.