Many congenital malformations often require a multidisciplinary and multistep surgical treatment, including the use of biological membranes. Aims of the study were to describe the use of these membranes for the correction of malformations, their clinical performance at follow-up, and patient's tolerance to them. The study included patients treated between 2009 and November 2020 in two referral centers. They were affected by abdominal wall defects (AWD), esophageal atresia/tracheo-esophageal fistula (EA/TEF), diaphragmatic hernia (CDH), spinal defects (SD), and anorectal malformations (ARM). The human origin membranes used during surgery were amniotic membrane, fascia lata, and pericardium provided by the local tissue bank and the porcine-derived membrane available on the market. Thirty-one patients were retrieved. The sample included 10 AWD, 7 EA/TEF, 5 CDH, 4 SD, 2 ARM, and 3 miscellaneous defects. The median age at repair was 139 days (range: 10,5–1494). The median follow-up was 1021 days (range: 485,5–1535). Two patients were lost at follow-up. The defects were successfully repaired and the membranes perfectly tolerated in 28/29 cases. In 1 case of CDH the fascia lata was replaced with a Goretex patch due to recurrence of the defect. This is the largest series on the use of biological membranes in congenital malformations. The variety of tissues allows to choose the best material for each malformation. The excellent tolerance and performance of this first series of patients encourage the use of these membranes to correct different type of malformations at any age.