The effect of both microwave (1000W-340s) and conventional heating (97°C-30s) on the quality and shelf-life of kiwifruit puree was investigated. The growth of microorganisms and the evolution of enzyme activity, colour, pH, bioactive compounds and antioxidant activity in the product during storage at 4, 10 and 22°C were checked. The storage temperature had a significant (p<0.05) impact on both the shelf-life and the nutritional and functional value of the samples: the higher the temperature, the significantly (p<0.05) faster the rate of both the sample spoilage and the loss of the bioactive compounds. On the other hand, thermal processing significantly (p<0.05) reduced the growth of microorganisms and the degradation rate of some bioactive compounds in a 12-59%, as well as leading to enzyme and colour stabilization. A longer shelf-life (123 days at 4°C) and a superior preservation of colour (δESE=6.54) and bioactive compounds (57-67%) were obtained when microwave heating was the technology selected to process the kiwifruit puree. Microwave heating was considered a suitable means of preserving kiwifruit puree that might be successfully employed as an innovation tool with which to help safe, high-quality and minimally processed kiwifruit based-products reach the market.