Municipal mud consists of organic matter naturally deposited in a microbial-rich environment, and its common pre-treatment in the laboratory is normally different from that in situ. In this study, an improved pre-loading method and the common pre-treatment method (by air or oven drying) were first applied to investigate the effect of microorganisms within organic matter on performance of the solidified soils. Results reveal that (i) Atterberg limits in the pre-loading method were higher than those in the drying method; (ii) the time-dependent strength became stable for the solidified soils pre-treated by the drying method, while strength decreased for the soils pre-treated by the pre-loading method; (iii) pH value of solidified soils by the pre-loading method decreased more significantly. After excluding the possible porosity influence on solidified soils, the effects of microorganisms within organic matter were investigated by microbial identification tests, including fluorescence detection and high-throughput sequencing. The pre-treatment procedure changed the vitality and diversity of microorganisms, leading to a rebalance between acid erosion and cement hydration during long-term curing. At the end, the long-term strength of the solidified municipal mud by the traditional pre-treatment method (by air or oven drying) could be overevaluated.