We have developed an organic solvent-free process to enrich natural antimicrobials from the important Nordic Rubus berry species, especially from cloudberry. The process utilizes industrial berry byproducts as raw-material, and it is based on seed sanding technology and water-based extraction. The extracts showed strong antimicrobial activity against Gram-positive Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA). A concentration of 5 mg/mL totally eliminated these bacteria in 24 h. Effects against Gram-negative bacteria were modest. Polyphenol analysis of the hydrothermal extracts showed that the antimicrobial activity is correlated to ellagitannins, mainly dimeric sanguiin H-6 and sanguiin H-10 isomers. Sanguiin H-10 is not commonly found in intact cloudberry seeds, but it is formed from the dimeric and trimeric ellagitannins, during the extraction. Surprisingly hydrothermal extracts had no or minor effects on beneficial bacteria, Lactobacillus rhamnosus. This interesting finding might offer an application potential in controlling skin microbial pathogens, for example, in wound healing.