Cnidarians are a diverse clade of marine invertebrates that inhabit a variety of environments. The conditions of these habitats are becoming more extreme with the progression of time. These organisms associate with bacteria, which are composed of a larger community, known as the microbiome. To better understand the interactions between individual bacterial isolates and the model cnidarian Nematostella vectensis, it is imperative to investigate and develop methodologies. Here, the impacts of antibiotics were quantified throughout the life stages with a variety of methods. Antibiotic treatment effectively eliminates the resident bacteria of N. vectensis, though the anemone experiences transcriptional changes, even after removal of the antibiotics. Additionally, two methods to vector bacteria to the terminal host were quantitatively compared: Prey Feeding Method (PFM), and Solution Uptake Method (SUM). The PFM resulted in higher sustained concentrations through two weeks, indicating its potential as a viable method to vector bacteria. Lastly, part of the culturable microbiome was assessed for viability through thermal and saline stressors. Investigation of these methods is imperative to quantifying the interactions between bacteria and the host organism. Together, the assessment of common methodologies in a cnidarian model contributes directly to understanding individual bacteria from the microbiome of N. vectensis.