Endosymbiotic Wolbachia bacteria infect divergent arthropod and nematode hosts. Many strains cause cytoplasmic incompatibility (CI) that kills uninfected embryos fertilized by Wolbachia-modified sperm. Infected embryos are protected from CI, promoting Wolbachia spread to high equilibrium frequencies balanced by imperfect maternal transmission. CI strength varies widely in nature and tends to decrease as males age. Understanding the causes of CI-strength variation is crucial to explain Wolbachia prevalence in host populations. Here, we investigate how fast and why CI strength decreases with male age in two model systems: wMel in Drosophila melanogaster and wRi in D. simulans. Average wMel CI strength decreases rapidly (19%/ day), and wRi CI strength decreases slowly (6%/ day) as males age; thus, within three days, wMel-infected males do not cause CI, whereas twelve-day-old wRi-infected males still cause minor, yet significant, CI. We tested if reductions in Wolbachia densities or CI gene expression as males age could explain this pattern. Indeed, wRi densities and CI gene expression decrease in testes as males age, but wMel densities and CI gene expression surprisingly increase with male age as CI strength decreases. Phage WO lytic activity and wMel Octomom copy number-an ampliconic gene region that influences wMel proliferation-do not explain age-dependent Wolbachia densities. However, the expression of Relish, an essential gene in the Drosophila immune deficiency pathway, strongly correlates with wMel densities. Together, these results suggest that testes-wide Wolbachia density and CI gene expression are insufficient to explain age-dependent CI strength across strains and that Wolbachia density is variably impacted by male age across Wolbachia-host associations. We hypothesize that host immunity may underlie variation in age-dependent density dynamics. More broadly, the rapid decline of wMel CI strength during the first week of D. melanogaster life likely contributes to wMel frequency variation observed on several continents.