Whether the association between UPF intake and body weight persists after accounting for dietary quality remains unclear. This analysis examined whether UPF intake is associated with BMI after adjustment for diet quality and whether a threshold exists above which diet quality deteriorates. Demographic and anthropometric data were collected from 307 adults in Greece (December 2022 to January 2024). Dietary intake was assessed using 24 h recalls. UPF intake was expressed as a percentage of energy, and diet quality was evaluated using the Healthy Diet Indicator 2020 (HDI-2020). Multivariable regression examined UPF intake and HDI associations with BMI, adjusting for age, gender, energy intake, smoking, and education. Linear, quadratic, and segmented models examined UPF–HDI associations and thresholds. Higher UPF intake was associated with higher BMI after adjusting for HDI and covariates (B = 0.022 kg/m² per 1% of energy from UPF, 95% CI 0.005–0.040, p = 0.013), whereas HDI was not associated with BMI (p = 0.081). No significant UPF × HDI interaction emerged (p = 0.267). UPF was inversely associated with HDI (p < 0.001), with no threshold within the observed exposure range. Findings suggest an association of UPF intake with BMI after diet-quality adjustment, while its inverse association with HDI appears linear.