Microgreens are tender leafy vegetables which are popular among consumers due to their pleasing colors, textures, flavors, and high nutritive values. Microgreens are generally consumed fresh and in relatively large portion sizes. Tender cotyledons of carrot, beetroot, lettuce, amaranthus, cabbage etc. are popular as microgreens among local consumers at present. All most all exotic vegetable seeds found in domestic markets are treated with fungicide (Thiram: Tetramethylthiuram disulfide) thus pose a health risk. Therefore, this study was conducted to identify the presence of fungicide residue in 3 microgreen varieties Amaranthus (Amaranthus viridis; var Red Thampala), Carrot (Daucus carota subsp. sativus; var New Kurodaand and Mungbean (Vigna radiata; var MI 5). Seeds were sawn at 125 g/m2 rate on trays with a coir dust medium and 30-36 LUX light was supplied continuously. Temperature, pH and RH of the growth medium were maintained at 28–30 °C, 5.5–6.0 and 90–95% while 70–78 % RH and 30–34 °C temperature were maintained as environmental conditions. Height at harvesting of 10 – 14 days old carrot and amaranthus microgreens were 7.5 cm while that of mungbean was 14 cm. Chlorophyll content and fungicide residue were analyzed in harvested microgreens and microbial growth of growth medium was checked. Amaranthuss and carrot had 1.1 CCI and mungbean had 2.4 CCI values as average chlorophyll contents at harvesting. According to FTIR analysis thiram presented only in carrot microgreens and further quantifications are on progress. Mean results of standard plate count of growth medium were 10 CFU/ml in amaranthus and 11 CFU/ml in carrot and mungbean.