In this study, for the first time, to confirm the effect of bacterial growth phase on the malachite flotation were investigated in a well-controlled Hallimond tube system. The test results showed that the bacteria in the stationary phase exhibit two-fold greater floatability than those in mid-exponential phase. To understand the observed flotation behavior, complementary cell characterization tests and cell attachment tests were conducted. Interestingly, the bacteria at both phases exhibited similar surface properties as well as almost identical amount of cells attached onto the malachite, suggesting that the growth phase-dependent flotation behavior cannot be attributed to the variation of cell surface properties and the extent of cell adsorption. On the other hand, cell detachment tests revealed that the amount of cells detached from the malachite surface is greater for the mid-exponential phase than the stationary phase due to the higher fluid drag applied to the cells at the mid-exponential phase, which was explained by the differences in the size and shape of attached bacteria onto the malachite surface. These morphological characteristics were found to cause the bacteria of mid-exponential phase to be separated highly sensitive and easy from malachite surface due to the fluid flow. Second, scale-up selective bioflotation tests were carried out in a 1 L Denver cell in malachite–silica binary mixture systems. Through the tests, we optimized the cell concentration and the malachite fraction in the feed. Overall, high malachite selectively was observed under optimized conditions (both recovery and grade showed more than 90%). The trend was in agreement with classical DLVO interaction energy profiles, which show the relative magnitudes of the adhesive forces between the mineral and the attached cell under equal hydrodynamic conditions.