Acinetobacter baylyi ADP1 is an ideal bacterial strain for synthetic biology and metabolic engineering due to its high natural transformability and capability for processing diverse chemical compounds. For the production of compounds within industrial bioreactors, it is optimal to have a uniform dispersal of bacterial cells within solution, but mutations in bacterial cells may generate surface properties leading to cell aggregation. During long-term culture in the laboratory, mutants of the bacterium A. baylyi ADP1 originated a distinctive phenotype of cell aggregation. Genome sequencing and the analysis of gene knockouts showed this aggregation to be due to mutations in the per and pgi genes, and a reduction in bioemulsifier production. Qualitative analysis of Atomic Force Microscopy (AFM) visualizations identified altered appearances of cell surfaces correlating with the difference in cell aggregation phenotype. AFM force spectroscopy experiments were then conducted to compare the adhesive and viscoelastic properties of aggregating cells to non-aggregating cells. The most distinctive difference found for force spectroscopy measurements was for a four-fold difference in nN in adhesion that was attributable to pgi. Overall, this experiment has resulted in a multilevel approach for the evaluation and detection of a cell aggregation phenotype in mutant strains of A. baylyi ADP1.