Microgreens can be contaminated by various preharvest sources including soilless substrate, plant nutrition solution, water and seeds. The aim of this study was to determine the transfer level of Salmonella, Shiga toxin-producing Escherichia coli O157:H7, and Listeria monocytogenes to the edible part of various type of microgreens from plant nutrient solution-soaked perlite as soilless substrate or seeds. Ampicillin resistant 3-strain cocktails of Salmonella and E. coli O157:H7 and non-resistant L. monocytogenes were independently inoculated into plant nutrient solution-soaked perlite and seeds in low (102–103 CFU/g) and high (105–106 CFU/g) populations. Twenty types of microgreens were grown in inoculated perlite. The seed inoculation was performed on five types of microgreens. Correlations between pathogen transfer levels with seed characteristics and harvest time were assessed. Pathogen populations (1.6 ± 0.2 to 7.7 ± 0.1 log CFU/g) transferred to microgreens were dependent on type of pathogen and microgreen but not affected by contamination source and inoculation level. The level of pathogen transferred to microgreens had a moderate to high negative correlations (R2) with seed surface area (−0.551 to −0.781), seed weight (−0.735 to −0.818), and harvest time (−0.332 to −0.919) when grown in Salmonella and E. coli O157:H7 inoculated perlite. This study suggests a high risk of pathogen population transferring to microgreens in case of seed or soilless substrate contamination when pathogen growth or survival is supported in plant nutrient solution. Display omitted •Pathogens were transferred to 20 types of microgreens regardless of inoculation level.•Transfer level depended on types of pathogens, microgreens, and contamination source.•Microgreens with epigeal seed germination had higher transfer than hypogeal types.•Seed surface area/weight and days to harvest correlated with pathogen transfer level.•Pathogen transferred to microgreens had negative correlation to seed size.