In clinical practice, caregivers of children with phenylketonuria (PKU) report that their children have breath malodour. This might be linked to the regular consumption of low phenylalanine (Phe)/Phe-free protein substitutes (PS), which are an essential component of a low-Phe diet. Oral malodour can negatively affect interpersonal communication, lead to bullying, low self-esteem and social isolation. In this longitudinal cross-over study, exhaled volatile organic compounds (VOCs) were measured using gas chromatography-ion mobility spectrometry. 40 children (20 PKU, 20 controls) were recruited. Subjects with PKU took either L-Amino Acid (L-AA) or Casein Glycomacropeptide (CGMP-AA) exclusively for 1 week, in a randomised order. On the seventh day, seven exhaled breath samples were collected over a 10 h period. Subjects then transferred to the other PS for a week and on day seven, provided seven further breath samples. All subjects had a standardised menu using low-Phe food alternatives and all food intake was measured and recorded. In the PKU group, the aim was to collect samples 30 min after consuming PS. In 3 subjects, breath was collected 5 min post-PS consumption. Fasted L-AA and CGMP-AA breath samples contained a similar number of VOC peaks (10-12) as controls. Longitudinal breath testing results demonstrate that there was no significant difference in the number of exhaled VOCs, comparing L-AA or CGMP-AA with controls, or between PS (12-18 VOC peaks). Breath analysed immediately after consumption of PS (n = 3) showed an immediate increase in the number of VOC peaks (25-30), but these were no longer detectable at 30 min post-consumption. This suggests PS have a transient effect on exhaled breath. Measurements taken 30 min after consuming L-AA or CGMP-AA were not significantly different to controls. This indicates that timing food and drinks with PS consumption may be a potential solution for carers to reduce or eliminate unpleasant PS-related breath odours.