To better understand the microbial quality and safety of plant-based meat analogues, this study investigated the changes of native microflora present in soy- and pea-based meat analogues (SBM and PBM) and compared them with ground beef (GB). SBM, PBM, and GB were also artificially inoculated with meat spoilage microorganisms, Pseudomonas fluorescens and Brochothrix thermosphacta, and pathogenic microorganisms, Escherichia coli O157:H7, Salmonella spp., and Listeria monocytogenes; the fitness of these bacteria was evaluated during storage at refrigerated and/or abused temperatures. Results showed that the initial total aerobic plate count (APC), coliform, lactic acid bacteria (LAB), and mold/yeast (M/Y) counts for GB could be as high as 5.44, 2.90, 4.61, and 3.45 log CFU/g, while the highest initial APC, coliform, LAB, and M/Y counts found in SBM were 3.10, 2.00, 2.04, and 1.95 log CFU/g, and were 3.82, 2.51, 3.61, and 1.44 log CFU/g for PBM. The batch-to-batch differences in microbial counts were more significant in GB than in SBM and PBM. Despite the different initial concentrations, there was no difference among APC and LAB counts between the three meat types by the end of the 10-day 4 °C storage period, all approaching ca. 7.00 log CFU/g. Artificially-inoculated B. thermosphacta increased by 0.76, 1.58, and 0.96 log CFU/g in GB, PBM, and SBM respectively by the end of the refrigeration storage; P. fluorescens increased by 4.92, 3.00, and 0.40 log CFU/g in GB, PBM, and SBM respectively. Under refrigerated storage conditions, pathogenic bacteria did not change in GB and SBM. L. monocytogenes increased by 0.74 log in PBM during the 7-day storage at 4 °C. All three pathogens grew at abused storage temperatures, regardless of the meat type. Results indicated that plant-based meat could support the survival and even growth of spoilage and pathogenic microorganisms. Preventive controls are needed for ensuring the microbial quality and safety of plant-based meat analogues.