The impact of crack orientation on healing in conventional mortar and bacteria-based bio-mortars was assessed under submerged marine conditions. The bacteria-based bio-mortar was prepared using Halobacillus Halophilus bacteria, expanded perlite aggregates and calcium lactate. Cracks were divided into five groups based on their orientation. Upward-faced and side-faced horizontal cracks in conventional mortar showed maximum overall healing of 77 %–90 % for the analysed crack range. Downward-faced and side-faced vertical cracks had three and four times less autogenous healing than upward-faced cracks, respectively; however, their healing doubled with the addition of bacteria. The variation in healing performance with orientation was explained by differences in the deposition of healing products under gravity. Additionally, healing products were also found within the cross-section of cracks in horizontally-placed bacteria-based specimens. Although their formation initiated away from the centre, after 35 days of exposure, the maximum healing was observed close to the centre spreading to the top surface of these bio-mortar specimens. These outcomes imply that results in literature must be carefully interpreted. This phenomenon of healing dependency on crack orientation is rarely studied and might have unknowingly affected the interpretation of the results in previous studies.