This study assessed the effects of diet supplementation with industrial processing by-products of acerola (Malpighia emarginata D.C.), cashew (Anacardium occidentale L.) and guava (Psidium guajava L.) fruit on the intestinal health and lipid metabolism of female Wistar rats with diet-induced dyslipidaemia. Female rats were randomly divided into five groups: healthy control, dyslipidaemic control and dyslipidaemic experimental receiving acerola, cashew or guava processing by-products. Fruit processing by-products were administered (400 mg/kg body weight) via orogastric administration for 28 consecutive days. Acerola, cashew and guava by-products caused body weight reduction (3·42, 3·08 and 5·20 %, respectively) in dyslipidaemic female rats. Dyslipidaemic female rats receiving fruit by-products, especially from acerola, presented decreased faecal pH, visceral fat, liver fat and serum lipid levels, as well as increased faecal moisture, faecal fat excretion, faecal Bifidobacterium spp. and Lactobacillus spp. counts and amounts of organic acids in faeces. Administration of the tested fruit processing by-products protected colon and liver from tissue damage (e.g. destruction of liver and colon cells and increased fat deposition in hepatocytes) induced by dyslipidaemic diet. Dietary fibres and phenolic compounds in tested fruit by-products may be associated with these positive effects. The industrial fruit processing by-products studied, mainly from acerola, exert functional properties that could enable their use to protect the harmful effects on intestinal health and lipid metabolism caused by dyslipidaemic diet.