A phenylalanine-restricted diet, supplemented with protein substitutes (PSs), remains the cornerstone of phenylketonuria (PKU) management. However, adherence is challenging in adulthood, and data on the nutritional status of early and continuously treated adults with PKU (ETAwPKU) are scarce. A total of 34 ETAwPKU (16 females; mean ± SD, age: 28 ± 9 years, phenylalanine concentration: 847 ± 285 µmol/L) and 34 age- and sex-matched control subjects were compared regarding their blood nutrient status, self-reported dietary intake, and cognitive wellbeing. Though diet adherence varied, all ETAwPKU were taking a PS. No significant differences were found for blood DHA, calcium, ferritin, transferrin, and zinc concentrations. However, selenium and ubiquinone concentrations were 16% and 29% lower in ETAwPKU, respectively (p < 0.01 and <0.0001). Vitamin concentrations (D, B12, B6, and folic acid) were significantly higher in ETAwPKU except for alpha-tocopherol. Amino acid (AA) concentrations differed between ETAwPKU and controls: they were significantly lower for 12 AAs and higher for phenylalanine and glycine. ETAwPKU had a significantly higher intake of most minerals and vitamins, except for niacin and phosphorus (no difference). Depending on the nutrient, PSs represented 52–100% of patients’ daily intake and 19% of total daily energy intake. Compared with controls, ETAwPKU scored significantly lower in three of the four subscales of the cognitive wellbeing questionnaire. Overall, the blood DHA and micronutrient status of ETAwPKU was adequate, except for selenium, with higher intakes than controls for most micronutrients. Patients relied heavily on PSs to meet the recommended intakes for protein, DHA, and micronutrients. The potential clinical impact of differences found in AA status should be further studied.