Studies were conducted to determine the effectiveness of isoeugenol (ISO-EU) at 0 (control) and 0.50, 0.75, 1.0 and 1.5 μL mL-1 for inactivating three enteric pathogens (Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella enterica) and indigenous spoilage microflora in Tyndallized and raw pineapple juice (PJ) respectively, during refrigerated (4 ᵒC) storage of the juice. Sub-lethal injury of pathogen survivors in PJ and the effect of ISO-EU on sensory characteristics of PJ were also evaluated. Batches of Tyndallized PJ with added ISO-EU and YEX (0.5% w/v) were each inoculated with a five-strain mixture of one pathogen to obtain ~7.1 log CFU mL-1. Non-inoculated batches of raw PJ were used for sensory analysis and monitoring the indigenous microflora namely, yeast and molds (YM), aerobic plate count (APC), lactic acid bacteria (LAB) and Enterobacteriaceae (ENT). Cultural methods using non-selective and appropriate selective agar media were used to enumerate microbial survivors. At 4ºC, all three enteric pathogens survived for more than 42 days in the control PJ; however, within 24 h, all ISO-EU treatments tested inactivated >5 log of each pathogen. After 2 h, ISO-EU treatments caused sub-lethal injury in survivors of all three pathogens. Initial populations of all four groups of indigenous microflora decreased significantly (P<0.05) in PJ containing ISO-EU and YEX with the most rapid decrease occurring in the ENT group. Although the appearance (color), odor and viscosity of both Tyndallized and raw PJ, each with ISO-EU (0.5 µL mL-1) and YEX, were acceptable, taste and overall acceptance of those juices were unsatisfactory (P<0.05). Sensory scores for all characteristics of ISO-EU-containing PJ were similar after 1, 14 and 28 days; however, after 28 days the color, odor, taste and overall acceptance of control (raw PJ) were unsatisfactory. Based on these results, ISO-EU (0.5 to 1.5 µL mL-1) combined with YEX has good potential for improving both microbial safety and shelf-life of refrigerated PJ although ISO-EU negatively affected taste of the juice. In this respect further research is needed to determine an optimum balance between microbial control and taste acceptability of PJ with added ISO-EU.