Simple SummaryWeaning is the most stressful event in pig production and is often associated with reduced performance, diarrhoea and piglet mortality. Currently, a high dose of zinc oxide (ZnO) is used to prevent weaning-related loss in productivity. However, the feeding of ZnO in weaner piglets will be phased out by 2022 in Europe, leaving pig producers without options to manage post-weaning disorders. This study investigated whether fermented rapeseed meal (FRM) alone or in combination with one (FRMA) or more (FRMAS) brown macroalgae species could improve weaner piglet growth, intestinal development and health compared to either non-supplemented diets (negative control, NC) or diets supplemented with 2500 ppm ZnO (positive control, PC). Both FRM and FRMA resulted in a similar production performance to PC when fed to weaned piglets. The PC, FRM and FRMAS (gender-specific) improved jejunal villus development more than the NC. Colon mucosal development was stimulated, and signs of intestinal inflammation were reduced by FRM. The composition and diversity of colon microbiota were similar between all fermented feeds and PC, but different compared to NC. In conclusion, FRM was at least as effective as ZnO to improve piglet growth, intestinal development and health.The feeding of medicinal zinc oxide (ZnO) to weaner piglets will be phased out after 2022 in Europe, leaving pig producers without options to manage post-weaning disorders. This study assessed whether rapeseed meal, fermented alone (FRM) or co-fermented with a single (Ascophylum nodosum; FRMA), or two (A. nodossum and Saccharina latissima; FRMAS) brown macroalagae species, could improve weaner piglet performance and stimulate intestinal development as well as maturation of gut microbiota in the absence of in-feed zinc. Weaned piglets (n = 1240) were fed, during 28–85 days of age, a basal diet with no additives (negative control; NC), 2500 ppm in-feed ZnO (positive control; PC), FRM, FRMA or FRMAS. Piglets fed FRM and FRMA had a similar or numerically improved, respectively, production performance compared to PC piglets. Jejunal villus development was stimulated over NC in PC, FRM and FRMAS (gender-specific). FRM enhanced colon mucosal development and reduced signs of intestinal inflammation. All fermented feeds and PC induced similar changes in the composition and diversity of colon microbiota compared to NC. In conclusion, piglet performance, intestinal development and health indicators were sustained or numerically improved when in-feed zinc was replaced by FRM.