Bacterial populations exhibit significant heterogeneity, even among genetically identical members of the same population, due to changes in gene expression. Individual variants, under certain selective pressures including environmental changes, antimicrobials or phages, can influence the evolutionary trajectory of a bacterial population. Phages target specific bacterial surface structures, and bacterial strategies such as the loss or modification of these receptors can prevent phage attachment, often through reversible changes in gene expression. However, such modifications can also alter the susceptibility to other phages or antibiotics. Understanding how bacterial heterogeneity influences phage–host interactions is crucial for studying coevolution and adaptation. While the study of resistance mechanisms often involves the isolation of phage-resistant variants, the transient nature of some bacterial phenotypes poses a challenge. This study proposes a cell sorting-based method to separate individual cells from heterogeneous populations and test their phenotypes under different treatments. We illustrate the application of this protocol with a representative bacterial culture infected by a single phage, where resistant variants emerge and increase in frequency gaining sensitivity to another phage. The protocol allows for the estimation of resistant and sensitive cells to different treatments (e.g., phages), providing insight into the heterogeneity of bacterial cultures.