The global increase of aquaculture production has caused an escalating demand for alternative protein feed ingredients. Agro-industrial by-products such as sunflower meal are relatively abundant and cheap, but the content of antinutritional factors and fiber in the raw products reduce nutritional value and limit the inclusion levels in the feed for nutritionally demanding species, including salmonids. Solid-state fermentation is a microbial processing method with the potential to reduce the content of fiber and antinutritional factors and improve nutritional value in plant protein raw materials. In this study, Atlantic salmon (Salmo salar) at two commercial-like fish farms were fed experimental diets containing either 5 % non-fermented sunflower meal (as a control diet), 5 % fermented sunflower meal or 10 % fermented sunflower meal. The aim was to compare the effects of fermented sunflower meal on growth performance, gut microbiota, distal intestine histology and gene expression of Atlantic salmon under different environmental conditions. The field trial lasted for 8 and 11 months in a coastal and fjord location, respectively. The findings revealed that diets with fermented sunflower meal sustained growth performance, improved intestinal health by reducing the prevalence of prominent inflammation and ectopic goblet cells, as well as down-regulated the expression of physiological pathways related to tissue damage and cell division. Additionally, 10 % fermented sunflower meal promoted the relative abundance of gut lactic acid bacteria Lactiplantibacillus and Lactobacillaceae after long-term feeding. Our results suggest that fermented sunflower meal is a suitable protein source for Atlantic salmon when included at a level of up to 10 % in the diet.