Manipulating the forces of selection can steer phage evolution toward desired ends, such as expanding host range of phages for phage therapy applications. Appelmans method is a passage-based protocol for expanding host range where a mixture of phages are distributed onto hosts—some permissive and some nonpermissive—in separate wells of a plate, incubated, and pooled again after growth before repeating. We sought to test if this method would effectively expand host range of phages that target Pseudomonas aeruginosa by passaging three phages (for nine iterations) on five strains of P. aeruginosa—three permissive and two nonpermissive. After only two rounds of passaging, host range expanded onto the nonpermissive hosts. Whole genome sequencing of phages isolated from Appelmans allowed for the identification of mutations compared to parent phages, although surprisingly, no mutations were found in known tail fiber genes as anticipated. Sequencing data also revealed that induction and evolution of prophages from two different bacterial hosts used in Appelmans had occurred, and contributed to variation of host range. Similar results were also observed when Appelmans was utilized to evolve phages against Paenibacillus larvae, the etiological agent of American Foulbrood disease in honeybees. These unexpected results of prophage induction and evolution during Appelmans demonstrate the advantages of generating complete reference genomes of bacterial host strains intended for directed evolution purposes. It also provides insight into the potential of prophage “contamination” of phage lysates, which could have negative impacts in the case of transduction of harmful bacterial genes, but may also have positive impacts such as the generation of virulent mutants of prophage with improved host ranges.