Phthalates and bisphenols, ubiquitous compounds found in various everyday products, have garnered attention due to their potential health-disrupting effects. This study aimed to (1) investigate urinary phthalate metabolites and bisphenol A (BPA) levels in donors and recipients prior to allogeneic hematopoietic stem cell transplantation (HSCT) and monitor changes in these compounds in pediatric recipients at different time points (day-9, day 0, day+7, day+28, day+90), and (2) assess their association with engraftment success. Urine samples from pediatric recipients and donors were collected for analysis of phthalate metabolites and BPA in 34 donor-recipient pairs. Monomethyl phthalate metabolite was not detectable in any of the urine samples. A notable increase in phthalate metabolites and BPA levels was observed in recipients starting from day+28. Granulocyte engraftment time showed a positive correlation with donor urinary levels of mono-n-butyl phthalate (MBP), mono-2-ethylhexyl phthalate (MEHP), and monobenzyl phthalate metabolites with recipient MBP levels measured on day-9. Moreover, donor urinary MBP and MEHP levels were also linked to delayed platelet engraftment. No relationship was observed between engraftment timing and the urine levels of monoethyl phthalate metabolite or BPA in donor-recipient pairs. In cases of mucositis, MEHP and MEP levels on day 0 were higher compared to the non-mucositis group. No relationship was identified between hemorrhagic cystitis and the levels of urine phthalate metabolites or BPA. These findings highlight the potential role of plasticizer exposure in influencing engraftment outcomes, although no significant associations were found between MEP or BPA levels and engraftment.