Postharvest loss of tomato is high globally as well as locally in Ethiopia. The losses are due to physiological changes, microbial spoilage, mechanical injuries, and lack of suitable handling and storage mechanisms. In this work physiological and microbial quality attributes of tomato fruits treated by soaking in spice extracts and kept in zeolite impregnated packaging films (perforated and non-perforated) were assessed for four weeks. The spice extracts (cinnamon, clove, and their mixture) were used mainly for their antimicrobial effects and zeolite (zeolite 4A) in low density polyethylene (LDPE) packaging films is important in the absorption of ethylene gas, which is the main hormone that accelerates ripening of climacteric fruits like tomato. Thickness, tensile strength, opacity, color intensity, and thermogravimetric analyses of the films were conducted to evaluate their importance as packaging material. Packaging films with 7% zeolite have shown to reduce physiological changes (weight loss, firmness, total carotenoid content, and color index) of tomato significantly (p<0.05) more than packaging films with 4% zeolite. Moreover, films with 4% zeolite are also better in keeping these physiological quality changes than packaging films with 0% zeolite. Spice extracts also tend to reduce these physiological changes of the fruit slightly. From the microbial analyses, clove extract was found to be more antibacterial and cinnamon was more antifungal. Based on the interaction effect (p<0.05) of the extracts and zeolite impregnated packaging films, the sample treated with cinnamon extract and kept in perforated 7% zeolite packaging film is more acceptable in terms of physiological and microbial quality aspects. In the fourth week, it had the lowest percentage weight loss and highest firmness, which are 5.76% and 104.86N/cm2, respectively. Its carotenoid content is 65.47µg/g and color index, 1.45. It had 15.1×104 cfu/g total plate count and the lowest cfu/g for yeast and mould count (0.685×104). Generally, non-perforated packaging films are somewhat good for short storage period but for long storage of the tomato fruits, perforated packaging films are more preferable in terms of physiological and microbial quality parameters.