Wolbachia are maternally inherited symbionts that display a remarkable diversity of reproductive effects, inducing parthenogenesis in Bryobinae and cytoplasmic incompatibility and sex allocation distortion in Tetranychinae. While these reproductive phenotypes are expected to promote Wolbachia spread throughout a population, we still know little about how Wolbachia infection frequencies are structured in natural populations. Surveying Wolbachia infection frequencies of Tetranychus urticae revealed divergence across natural populations, raising the question of what underlies this frequency variation. Based on theory, Wolbachia spread through host populations via three key symbiosis traits: maternal transmission, fecundity, and the penetrance of reproductive phenotypes. Yet, how host and Wolbachia genotypes interact to shape each of these parameters remains poorly understood, making it difficult to predict where and why Wolbachia persist or are lost in the field. To address this, we first quantified Wolbachia maternal transmission across a broad panel of Tetranychus urticae lines, revealing substantial variation across host genotypes. 16S rRNA amplicon sequencing further showed that this variation spans multiple distinct Wolbachia strains across populations, implicating both host and symbiont genotype in shaping transmission. To dissect their relative contributions, we constructed a nuclear–cytoplasmic introgression panel in which three Wolbachia variants were introduced into two divergent near-isogenic host backgrounds. For every host-symbiont combination, we quantified all three determinants of infection frequency alongside Wolbachia infection density. We additionally quantified Wolbachia titer to assess whether variation in bacterial density contributes to differences in these parameters. Modelling the empirical data reveals strong and distinct contributions of both host and symbiont genotype across multiple parameters, demonstrating that the full complexity of infection frequency dynamics cannot be fully understood from the symbiont or host perspective alone. Together, our results advance the understanding of how host-symbiont interactions shape Wolbachia persistence and spread, and provide a framework for predicting infection frequency dynamics in natural populations.