(1) Background: This study aimed to evaluate the effect of an extruded whole-grain sorghum beverage containing L. paracasei on body composition, lipid profiles, and intestinal health in overweight and obese adults. (2) Methods: A chronic, single-blind randomized controlled pilot study was conducted with 30 volunteers allocated to three groups (n = 10/group): extruded sorghum beverage (ESB), extruded sorghum beverage with L. paracasei (ESPB), and control beverage (CB) (waxy maize starch). The chemical composition of the beverages was analyzed. Volunteers consumed the beverages for ten weeks at breakfast, along with individual dietary prescriptions. Body composition, biochemical markers, gastrointestinal symptoms, stool consistency, intestinal permeability, short-chain fatty acids, fecal pH, and stool L. paracasei DNA concentration were analyzed at the beginning and end of the intervention period. (3) Results: The ESB showed better composition than the CB, particularly in terms of resistant starch content, total phenolic compounds, condensed tannins, and antioxidant capacity. Both the ESB and the ESPB had an effect on body composition (estimated total visceral fat and waist volume), biochemical markers (Castelli index I), and intestinal health (Bristol scale, diarrhea score, valeric acid, and L. paracasei DNA concentration). No changes were observed in the CB group after the intervention. (4) Conclusions: Whole-grain sorghum beverages demonstrated good nutritional value, and consumption of these beverages, with or without L. paracasei, provided health benefits, including improvements in body composition, Castelli index I scores, and intestinal health, in overweight and obese adults.