Abstract Prototheca spp. are parasitic algae that can infect humans, cattle, cats and dogs. Although it is rarely seen, if protothecosis occurs in dogs, it is often fatal due to dissemination of the algae and a poor response to treatment. A 3‐year‐old, Scottish Collie dog, female, neutered, was presented with large bowel diarrhoea, weight loss and lethargy of 2 months. The dog had also experienced a short transient episode of acute horizontal nystagmus, left‐sided head tilt and cervical pain 2 weeks before presentation. Histology of the colon demonstrated an erosive neutrophilic colitis with periodic acid–Schiff stain‐positive structures compatible with Prototheca spp. confirmed using polymerase chain reaction. Treatment with nystatin (100,000 IU orally every 8 hours) was unsuccessful, and euthanasia was performed soon after diagnosis. This case report documents the first reported case of canine protothecosis in the Netherlands, and demonstrates that nystatin treatment is not successful in every canine protothecosis case.