We conducted a pilot randomized clinical trial to examine the effects of the fasting-mimicking diet (FMD) on autophagic flux and metabolic health markers in healthy humans. Thirty healthy participants were randomized to two oral formulations of FMD (ProLon and FMD2) or control for 8 days. Blood was collected at baseline, days 4 and 6 during intervention, and 48 h after completing FMD (Day 8). Effects on autophagic flux were measured in peripheral blood mononuclear cells (PBMC) using the ratio of LC3B-II/LC3B-I protein in samples treated with chloroquine (CQ) ex vivo. Metabolic outcomes measured included fasting plasma glucose, insulin, insulin growth factor-1, β-hydroxy-butyrate (BHB), and insulin resistance (HOMA-IR). One-way ANOVA or Kruskal-Wallis tests were used to determine significant differences between groups, both at individual time points and changes from baseline to subsequent time points. Participants were 49.1 ± 11.8 years. Significant between-group differences were observed in changes from baseline to the end of the 6-day dietary intervention for body weight, fasting glucose, BHB, HOMA-IR, and autophagic flux (p < 0.05); however, differences were not significant across all time points. These results suggest that FMD may improve autophagic flux and markers of metabolic health. FMD may serve as a non-pharmaceutical intervention to modulate autophagy; however, further investigation with larger sample sizes is needed to confirm and extend these findings. This clinical trial was sponsored by L-Nutra Inc. and registered on ClinicalTrials.gov (NCT06115551).