Background/Objectives: Heavy metals are a group of metals and metalloids that have a relatively high density. They can cause toxicity even at very low levels. Trace elements are required by all living organisms to maintain their normal growth, metabolism, and development. Oral intake is the main route of exposure to both heavy metals and trace elements. Phenylketonuria (PKU) is the most common amino acid metabolic disorder, and the best known treatment for patients requiring treatment is a phenylalanine (Phe)-restricted diet. The objective of the present study was to evaluate the plasma heavy metal levels, sources of exposure, changes in these levels according to dietary regimen, and trace element levels and their correlations with heavy metals in PKU patients. Methods: The study was conducted between July 2022 and January 2024 on 105 patients aged 2–6 years diagnosed with PKU. Results: The percentage of Pb levels in individuals in the upper quartile increased by 3.47 times (95% CI = 1.07–11.29) in those who consumed canned foods and 7.29 times (95% CI = 1.21–44.03) in those who consumed spring water. The percentage of As levels in the upper tertile increased by a factor of 7.26 (95% CI = 2.09–25.28) in individuals under four years of age and 8.17 times (95% CI = 2.13–31.27) in canned food users. The odds of having blood Cd levels in the upper tertile were 0.09 (95% CI = 0.01–0.96) for those being breastfed for 6–11 months compared to 0–5 months. Zn levels were lower (93.0 vs. 83.6 µg/dL, p = 0.008) in patients on a Phe-restricted diet. Conclusions: The present study did not find a relationship between heavy metal exposure and the dietary treatment status of patients with PKU. Our findings indicate that canned food consumption is a significant contributing factor to heavy metal exposure in PKU patients. Furthermore, our findings revealed a relationship between age, perception of economic level, breastfeeding, kitchen equipment, and water usage and the levels of certain heavy metals.