Nutritional profile and management of patients with primary immunodeficiencies (PID) undergoing hematopoietic stem cell transplant (HSCT) has not been described in the literature. We aim to report the nutritional challenges and practices peculiar to this population before and after HSCT and suggest clinical pathways for their management. We conducted a single-centre retrospective study. Inclusion criteria were children aged less than 20 years with a diagnosis of PID who have undergone HSCT at the Royal Children's Hospital Melbourne since April 2014 with a minimal follow-up of 1 year. Nutritional parameters were collected in the pre-transplant period, at conditioning, and at 1, 3, 6 and 12 months post-HSCT. Descriptive analysis were used. Between April 2014 and December 2018, 27 children received 31 HSCT. Before transplant, 33% had a weight and/or height ≤ -2 standard deviations (SD). Forty percent required nutritional support before transplant: 33% had enteral nutrition (EN) while 7% required long-term parenteral nutrition (PN) due to intestinal failure. After transplant, although most children were started on EN, 82% required PN with a mean duration of 67 days. Mean time to full oral diet was 154 days. Pre-transplant mean weight and height were -0.57 SD and -0.88 SD respectively. After a decrease in anthropometric parameters the first 3 months post-transplant, progressive catch up was noticeable for weight (-0.27 SD) with no catch up for height at 1 year (-0.93 SD). Our work highlights the nutritional challenges and specificities of children with PID in the peri-transplant period. An approach to nutrition assessment and management in the pre- and post-transplant period is proposed.