The investigation of oxide ion conductivity in apatite germanates has attracted significant interest due to potential applications in SOFC electrolyte materials. These systems conduct via interstitial oxide ions, and a range of studies have indicated the importance of the GeO4 units in the conduction process. In this paper, we investigate the effect of boron incorporation on the structure and conductivity. Studies show that heat treatment of La10Ge6O27 with H3BO3 leads to an expansion in cell volume, attributed to incorporation of borate groups in the oxygen ion channels within the structure. For low levels of dopant i.e La10Ge6O27(BO1.5)0.5, a small enhancement in conductivity was observed attributed to a transition from a triclinic to a hexagonal apatite. For further increases in boron content, the conductivity was shown to decrease attributed to the blocking of the conduction pathway down the apatite channels. Interestingly, significant oxide ion conductivity was still observed, which provides the first experimental support for a secondary conduction mechanism perpendicular to the apatite channels proposed by prior modelling studies.