The publication investigated the decontamination process of porcine umbilical cord tissue using plasma functionalized liquid alone and in combination with ultrasound. The challenge was to achieve lasting and complete decontamination without damaging tissue integrity because viable mesenchymal stem cells were extracted in the following step. The dataset contains numbers of counted colony forming units (CFU) of cultured microorganisms after the different iteration steps of tissue decontamination. Each worksheet summarizes the numbers of one figure. Further, the dataset contains cell counts and the ratio of viable cells as detected by DAPI stain.