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Simple Summary: The sulfite contents from bleach in all commercially available mustard pickle products exceeded the allowable limit of food additives (30 ppm), with a failure rate of 100%. Although the samples contained no food pathogens, the high-throughput sequencing results revealed potential environmental contamination in samples. We assessed the microbial and chemical qualities and microbiomes of 14 mustard pickle products coded sequentially from A to N and sold in traditional Taiwanese markets. The results showed that the aerobic plate count and lactic acid bacteria count of commercially available mustard pickle products were 2.18–4.01 and <1.0–3.77 log CFU/g, respectively. Moreover, no coliform bacteria, Escherichia coli, Staphylococcus aureus, Salmonella spp., or Listeria monocytogenes were detected in any of the samples. Analysis of the chemical quality showed that the sulfite content of all samples exceeded 30 ppm, which is the food additive limit in Taiwan. Furthermore, the mean contents of eight biogenic amines in the mustard pickle product samples were below 48.0 mg/kg. The results of high-throughput sequencing showed that the dominant bacterial genera in sample A were Proteus spp. (25%), Vibrio (25%), and Psychrobacter (10%), in sample C they were Weissella (62%) and Lactobacillus (15%), in sample E it was Lactobacillus (97%), and in sample J it was Companilactobacillus (57%). Mustard pickle product samples from different sources contained different microbiomes. The dominant bacterial family was Lactobacillaceae in all samples except for sample A. In contrast, the microbiome of sample A mainly consisted of Morganellaceae and Vibrionaceae, which may have resulted from environmental contamination during storage and sales. The result of this work suggests it may be necessary to monitor sulfite levels and potential sources of bacterial contamination in mustard pickle products, and to take appropriate measures to rule out any public health risks. [ABSTRACT FROM AUTHOR]