This study evaluated the effect of Bacillus subtilis C-3102 (Calsporin®) addition to the diet on faecal characteristics and nutrient digestibility in healthy adult dogs. Sixteen Beagles received either a low-energy control diet (CON; 3.35 Mcal metabolisable energy (ME)/kg with 21.8, 27.9, and 50.3% ME as protein, fat, and nitrogen-free extractives (NFE), respectively) or the same diet supplemented with Bacillus subtilis at 1 × 109 CFU/kg diet as probiotic (PRO) for four weeks in a parallel design (eight dogs per diet). In the prior two weeks, all dogs received a high-energy diet (Advance Medium Adult, Affinity Petcare®, 3.81 Mcal ME/kg ME with 24.8, 41.2, and 34% ME protein, fat, and NFE, respectively). Faecal consistency, dry matter (DM), pH, and NH3 were analysed on fresh samples collected at the start and weekly throughout the study. Additional samples were collected for the determination of lactate and short-chain fatty acids (SCFA) on days 0 and 21. In week four, a five–day total faecal collection was conducted in six dogs from each diet for the determination of nutrient apparent digestibility. Dogs fed the PRO diet had more firm faeces (P = 0.011) than control dogs and a higher faecal DM content in the first two weeks (P < 0.05). Feeding the PRO diet resulted in a decline in NH3 over four weeks (P = 0.05) and in faecal pH in the first two weeks (P < 0.05) alongside an increase in SCFA content (P = 0.044), mainly acetate (P = 0.024). Faecal lactate did not differ between diets (P > 0.10). Dogs fed the PRO diet showed a higher apparent digestibility of fat (P = 0.031) and NFE (P = 0.038) compared to control dogs. Dog food supplementation with Calsporin® at 1 × 109 CFU/kg improved faecal quality, enhanced fat and carbohydrate digestibility, and contributed to the gut health of dogs by reducing gut ammonia and increasing SCFA content.