Froth treatment tailings (FTT) are a waste product of the bitumen extraction process from Alberta oil sands. FTT contains residual bitumen, diluents (naphtha or paraffinic), water, and sand containing the sulphide mineral pyrite (FeS2). FTT is deposited in tailings ponds and there is a risk that the pyrite in tailings undergo weathering when exposed to oxygen, producing acidic drainage. A key area of research is to understand the effects of material overlying FTT in acid generation. This will allow us to predict post-closure acid rock drainage (ARD) generation and/or GHG emissions from the FTT. In this study, two scenarios under which covering materials may contribute to ARD were assessed. These include: (1) FTT capped with peat and (2) FTT capped with quartz sand. Columns with quartz sand capped with peat were used as controls. Columns were water-saturated, and water was added every week from the top of each column, while water samples were collected from a port at the base of the columns. Samples were analysed weekly for water chemistry, and monthly for microbial analysis. In the columns where FTT was capped with quartz sand, changes in physicochemical parameters (i.e., decreases in solution pH, or increases in dissolved iron and sulphate concentrations) were observed. This suggests acid generation at the late stage of the tests, while other columns show a lesser degree of acid rock drainage. Analysis of the microbial community structure with 16S rRNA gene amplicon sequencing in the leachate from the columns was started when the geochemistry changes were observed in the columns. Results showed that peat or peat-covered FTT was dominated by methanogens (mainly Methanolobus zinderi, Methanosaeta pelagica (Aceticlastic methanogens) and Methanomicrobium mobile (hydrogenotrophs methanogens. On the contrary, quartz sands-capped FTT was dominated by acidophiles (members of sulphur-oxidizing or iron-oxidizing bacteria). Methanogens were abundant in the early (days 277–354) stage of the sampling period, while acidophiles were abundant in the late stage (days 354–644) of the sampling period. Overall, the changes in physicochemical parameters and microbial communities in these columns suggest the weathering of sulphide minerals in the columns.