Excess nitrogen, phosphorus and trace element losses from pig manure accelerate eutrophication and soil degradation. Probiotic Bacillus subtilis produces phytase, protease and other enzymes and postbiotics that may enhance nutrient retention, yet the influence of delivery matrix on environmental outcomes is unclear. Three hundred and eighty-four weaned pigs (Yorkshire × Landrace; 28 d) were assigned to four diets until 30 kg body weight: positive control (PC, complete diet), negative control (NC, no additives), BS (NC + 0.1% B. subtilis 87Y spores) and FR (NC + 8% rapeseed meal fermented with Bacillus subtilis 87Y). Apparent total-tract and ileal digestibility (AID), daily excretion and retention of macro- and micro-elements were determined over 72 d. FR pigs showed the greatest improvements: faecal nitrogen fell by 32% and urinary nitrogen by 29% versus NC, lowering total nitrogen output from 6.6 to 4.5 g pig/day. Total phosphorus excretion declined 39% (from 3.05 to 1.85 g pig/day) and calcium retention rose 187%. Faecal zinc and copper were reduced by 63% and 39%, respectively. FR increased AID of phosphorus (from 47 to 70%) and magnesium (from 22 to 43%) by > 20%-points; BS achieved intermediate gains. Predicted farm-gate savings equal 26 kg N and 3.6 kg phosphorus per 1 000 weaners. Embedding Bacillus subtilis in fermented rapeseed meal immobilizes enzymes and metabolites, protects spores and supplies prebiotic levan, delivering larger environmental benefits than free spores alone. Integrating this synbiotic into nursery diets simultaneously valorizes a regional oil-seed by-product, displaces imported soy, and helps swine operations meet nutrient-loss reduction targets.