Strawberries and raspberries are susceptible to physiological and biological damage. Due to the consumer concern about using pesticides to control fruit rot, recent attention has been drawn to essential oils. Microbiological activity evaluations of different concentrations of tested EOs (cinnamon, clove, bergamot, rosemary and lemon; 10% DMSO-PBS solution was used as a diluent) against fruit rot fungal strains and a fruit-born human pathogen (Escherichia coli) indicated that the highest inhibition halos was found for pure cinnamon and clove oils; according to GC-MS analysis, these activities were due to the high level of the bioactive compounds cinnamaldehyde (54.5%) in cinnamon oil and eugenol (83%) in clove oil. Moreover, thermogravimetric evaluation showed they were thermally stable, with temperature peak of 232.0 °C for cinnamon and 200.6/234.9 °C for clove oils. Antibacterial activity evaluations of all tested EOs at concentrations from 5–50% (v/v) revealed a concentration of 10% (v/v) to be the minimum inhibitory concentration and minimum bactericidal concentration. The physicochemical analysis of fruits in an in vivo assay indicated that used filter papers doped with 10% (v/v) of cinnamon oil (stuck into the lids of plastic containers) were able to increase the total polyphenols and antioxidant activity in strawberries after four days, with it being easier to preserve strawberries than raspberries.