An unusual authigenic origin for halloysite and gibbsite is reported in a stalactite from Agios Georgios Cave, Kilkis. This speleothem includes mostly pure calcite whereas minor areas of Mg-rich calcite and scarce dolomite are present in four growth phases. Abundant pores are created due to imperfect coalescence of the calcite crystals. Several of them contain detrital muscovite, which was presumably transferred from the dripping water, during the formation of speleothem and has been variably altered to halloysite. Several pores in the stalactite contain different mineral assemblages that we interpret as in situ: halloysite-7Å, halloysite + silica, gibbsite + silica and gibbsite. The breakdown of the muscovite and the formation of halloysite require acidic conditions, which we suggest to have been established by potassium solubilising microorganisms. The silica minerals include spheroidal assemblages or needle-like and blade-like quartz and can be explained by further dissolution of halloysite, under the same acidic conditions in the presence of microorganisms. In our model, the precipitation of gibbsite is the result of direct formation from muscovite, promoted from abundant and undisturbed water percolation, at moderately low pH, also induced by the presence of bacteria. Given that microbial activities promote: (1) breakdown of muscovite and formation of halloysite, silica, and gibbsite, and (2) formation of Mg-calcite and dolomite after calcite, then it is likely that two or more different microbial communities may exist in the same speleothem. The first creates mild acidic conditions, aiming at the decomposition of muscovite in the microenvironment of the pores antagonising the second that produces alkaline microregimes and the local precipitation of Mg-rich carbonate minerals.