As coral bleaching events are intensifying because of climate change, effective strategies mitigating bleaching are urgently needed. One proposed strategy is the inoculation of corals with beneficial bacteria. Bacterial candidates have so far been selected based on functions expected to enhance coral heat tolerance. However, another important trait is that beneficial bacteria form a stable association with the coral host to ensure their benefits persist long-term. Here, we used 16S rRNA gene metabarcoding to study the temporal stability of four different bacterial candidates in each of two coral species, Galaxea fascicularis and Acropora loripes, over the course of five months in an aquarium setting. While the results of A. loripes are still being analysed, some candidates showed short-term update into G. fascicularis, but two persisted for five months. These results show that integration of bacterial candidates into the coral is not uniform. Combining this approach with a propidium monoazide treatment and digital PCR, we will also determine the viability and absolute quantity of bacterial candidates within in A. loripes. Applying beneficial bacteria with long-term viability within corals is essential for incorporating this intervention into coral reef restoration efforts, as repeated inoculations on large reef systems would be logistically impossible.