Interactions between macroalgae and corals are omnipresent on eutrophied and overfished reefs worldwide. Contact with macroalgae can disrupt corals and their microbiomes through diverse mechanisms, including shading, abrasion, and the release of algal exudates. However, changes in the coral microbiome after algal contact ceases have not been studied. We investigated the recovery of the microbiome of massive reef-building Porites corals following experimental removal of the overgrowing green macroalga Halimeda macrophysa. We followed changes in the microbiome of macroalgal-removed and adjacent healthy-looking tissue of coral colonies over 40 days. Coral tissue was predominantly bleached underneath the macroalgae but regained almost its full pigmentation by day 40. Despite this recovery in pigmentation, the bacterial microbiome of macroalgal-removed coral tissue did not return to that of adjacent healthy-looking tissue (control). Overall, macroalgal contact led to the suppression of Gammaproteobacteria and increased diversity and dominance of Alphaproteobacteria, a shift that persevered for 40 days after algal removal. Causal effect analysis showed a positive effect of influential OTUs in healthy-looking tissue assigned to Gammaproteobacteria and Bacteroidia on the relative abundance of other OTUs within these classes. The effect of influential OTUs assigned to Alphaproteobacteria in macroalgal-removed tissue on the relative abundance of other OTUs was more diverse. Despite the high heterogeneity of coral microbiomes, differences in the relative abundance of main bacterial classes and orders between control/healthy and macroalgal-removed tissue showed temporal patterns. Differences in the Alpha-, Gamma-, Deltaproteobacteria and Bacteroidia between control/healthy and macroalgal-removed tissue increased after cessation of macroalga contact and stabilized or declined towards day 40. Acidimicrobiia, Deltaproteobacteria, Rhodospirillales and Rhodovibrionales returned to average relative abundances in the adjacent control/healthy tissue after 40 days. Nevertheless, Rhizobiales and Rhodobacterales (Alphaproteobacteria) still dominated the macroalgal-removed microbiome on day 40. We conclude that macroalgal overgrowth induces changes in the coral microbiome, and that algal removal did not lead to full recovery of the microbiome in 40 days. Return of pigmentation and distinct shifts in bacterial groups over time appear a possible pathway to the recovery of the coral microbiome after macroalgal removal.