Pectin methylesterase (PME) in papaya nectar results in undesirable gel formation and peroxidase (POD) in strawberry nectar leads to nutrient loss, browning, and off-flavor production. Because of this, the effect of alternative processing techniques including ultra high temperature (UHT, 20-135°C, 1-3 s), high pressure processing (HPP, 20 or 60°C, 200-600 MPa) and irradiation (0-10 kGy) on PME and POD activity in papaya and strawberry nectar and their respective blends were compared to traditional thermal processing (80-130°C, 0-10 min). Traditional thermal (110°C, 5 min, 71.5% reduction) and UHT (110°C, 1-3 s, 98.0% reduction) processing were able to sufficiently reduce PME activity and prevent gel formation in papaya nectar. PME reduction was enhanced by synergistic reductions in nectar blends after UHT at 80°C. HPP was unable to prevent gel formation in papaya nectar, with enhanced activity at 400 MPa. Exposure of a blend 50P:50S to 10 kGy irradiation prevented gel formation. UHT enhanced POD activity at 110°C and synergistic reductions resulted for POD activity in nectar blends after irradiation. These findings highlight the benefits of alternative processing in reducing enzyme activity in fruit nectars and nectar blends.