Fish skin mucus is continuously replaced by epidermal cells, making it a highly dynamic microenvironment and an effective barrier against waterborne pathogens. The objective of this study was to understand the effects of tenacibaculosis, caused by the bacterium Tenacibaculum dicentrarchi, on the skin-associated microbiome of Atlantic salmon (Salmo salar). We used a vector-free and waterborne infection model of T. dicentrarchi strain TdCh05 in Atlantic salmon smolts for 21 days. Skin swab samples were collected at 2 h and 21 days post-infection (hpi and dpi, respectively) for 16S rRNA gene amplicon sequencing using DNA or complementary DNA (cDNA) as templates. Non-metric multidimensional scaling analysis grouped the samples into distinct clusters depending on the treatment and template. Similarity-Percentage (SIMPER) analysis indicated that between similar to 42% and 43% of the total amplicon sequence variants (ASVs) across all samples accounted for 90% of the compositional differences among all treatments and the two templates, highlighting the contribution of Tenacibaculum ASVs. Comparisons (by SIMPER) between non-infected and TdCh05-challenged fish at 2 hpi indicated that Tenacibaculum ASVs contributed to between similar to 52% and 58% of the differences in compositional clustering between samples. A significant drop in skin-mucus alpha diversity in TdCh05-challenged fish was also detected, followed by alpha diversity recovery at 21 dpi. In turn, at 21 dpi, microbiome changes were related to higher interaction complexity among taxa and community instability. Furthermore, 16S cDNA-based sequencing indicated that the potential activity of the Atlantic salmon skin-associated microbiome during disease progression was primarily driven by Tenacibaculum spp. Further research is needed to elucidate the role of other potentially active components (e.g., Pseudomonadales) of the skin-associated microbiome for the onset and/or progression of tenacibaculosis.