There is increasing interest in the utilization of tartary buckwheat (TB) for making various fermented foods due to its unique starch structure and functional features. However, studies on Daqu starter produced with TB as a raw material are lacking. This study aimed to compare the differences between conventional low-temperature Daqu (NDQ; 65% barley and 35% pea) and Daqu made with TB (BDQ; 55% barley, 30% pea, and 15% TB) in physicochemical properties, microbial communities, and volatile and nonvolatile metabolites. Compared with NDQ, BDQ exhibited higher saccharifying power, liquefying power, acid protease activity, and lower pH value. High-throughput sequencing revealed that the microbial community structure of NDQ and BDQ had significant differences. NDQ were enriched in Kroppenstedtia, Bacillus, Saccharomycopsis, Issatchenkia, Cladosporium, and Aspergillus, while BDQ were dominated by Kroppenstedtia, Comamonas, Pseudomonas, Acinetobacter, Rhizopus, and Saccharomycopsis. There were notable distinctions in volatile and nonvolatile metabolomic profiles between NDQ and BDQ. The physicochemical differences between NDQ and BDQ were driven by their different microbiota, which also led to the inconsistency of their metabolite profiles. The bacterial community was significantly correlated with pH and acid protease activity, whereas the fungal community was only strongly correlated with saccharifying power. In addition, the correlation network demonstrated that the resident dominant microbes in Daqu had strong connections to numerous important volatile and nonvolatile compounds. This study provided a detailed insight into the microbiome characteristics that differ between the NDQ and BDQ, and it can be helpful to develop a TB-based starter applied in making traditional fermented foods.