Background: Obesity is associated with metabolic dysregulation, mood disturbance, and poor sleep quality. Although dietary fiber and probiotic supplementation have both been proposed as microbiome-targeted strategies for obesity management, their independent and combined effects remain unclear. Methods: In this double-blind, randomized, placebo-controlled 2 × 2 factorial trial, 56 adults with obesity were randomized to placebo, dietary fiber, probiotic, or combined supplementation for 8 weeks. One withdrew during baseline assessment, and 55 participants were included in the intention-to-treat analysis. Outcomes included metabolic syndrome-related indicators, mood assessed by the Profile of Mood State, and sleep quality assessed by the Pittsburgh Sleep Quality Index. Intervention effects were evaluated using factorial ANCOVA with baseline adjustment. Results: No significant dietary fiber × probiotic interactions were detected. Dietary fiber supplementation showed selective favorable effects, mainly on HDL cholesterol and mood-related outcomes. Probiotic supplementation showed a significant main effect primarily on HDL cholesterol but did not remain significant after FDR correction. Sleep-related improvements were observed only in within-group analyses and were not supported by significant factorial ANCOVA effects. Combined supplementation did not provide additional benefits over single-component interventions. Conclusions: Dietary fiber supplementation may have selective favorable effects in adults with obesity, particularly on HDL cholesterol and mood-related outcomes. The absence of additional benefit from combined supplementation suggests that the effectiveness of synbiotic strategies may depend on the compatibility between the selected dietary fiber and probiotic strains.