The retail market is the largest domestic unwashed chicken egg market in Taiwan. Being unwashed, contamination may be introduced, and internal pathogens may grow during the collection, distribution, transport, and storage stages of the eggs. Microbial safety is an important factor contributing to egg quality. The purpose of this study was to assess the microbial profiles of the shell surface and internal fraction of retail washed and unwashed shell chicken eggs in Taiwan, to better understand the microbial safety and quality of retail eggs. A total of 210 unwashed and 57 washed eggs were collected and screened between July 2019 and January 2020. Pathogenic E. coli, Salmonella spp., and S. aureus were not detected in any of the sampled eggs. The prevalence of Staphylococcus spp. and Enterobacteriaceae on the surface of unwashed shelled chicken eggs was 93.81% and 13.33%, respectively. Of the unwashed shelled chicken eggs, 197 samples were positive for Staphylococcus spp., and 28 samples were positive for both Staphylococcus spp. and Enterobacteriaceae, among which four eggs were contaminated with higher levels of Enterobacteriaceae (13,000–365,000 CFU/egg) than others. On the internal fraction of unwashed shelled chicken eggs, the prevalence of Staphylococcus spp., Enterobacteriaceae and E. coli was 1.90%, 1.90%, and 0.48%, respectively. Staphylococcus spp. were detected in four samples. Enterobacteriaceae were found in four other samples, with non-pathogenic E. coli in one of the four egg samples. The prevalence of Staphylococcus spp. and Enterobacteriaceae on the surface of washed eggs was 66.67%, and 7.02%, respectively, and there were no Enterobacteriaceae, Staphylococcus spp., E. coli, S. aureus, or Salmonella spp. in the contents of washed eggs. Staphylococcus spp. were more dominant in unwashed and washed eggshells compared to Staphylococcus spp. and Enterobacteriaceae in the content of unwashed eggs. The Enterobacteriaceae and Staphylococcus spp. counts were considerably higher in unwashed eggs than in washed eggs. For unwashed egg samples, the Enterobacteriaceae counts ranged from 10 to 365,000 CFU for eggshells and two to 14,600 CFU for egg contents; the Staphylococcus spp. counts ranged from three to over 1,100 MPN for eggshells and 0.3 to 3.6 MPN for egg contents. These results indicate that washed eggs have better microbial safety and quality in Taiwan. Effective control measures are also recommended for unwashed eggs.