In general, fruit consumption in the EU does not meet governments’ recommended levels, and innovations in the fruit industry are thought to be useful for increasing fruit consumption. Despite the enormous number of product innovations, the majority of new products in the market fail within the first two years, due to a lack of consumer acceptance. Consumer segmentation may be a useful research tool to increase the success rates of new fruit products. The current study aims to identify consumer segments based on individual importance rankings of fruit choice motives. We conducted a cross-national, online panel survey on fresh fruit innovations in four European countries: the Netherlands (n = 251), Greece (n = 246), Poland (n = 250), and Spain (n = 250). Our cluster analysis revealed three homogeneous consumer segments: Average Joe, the Naturally conscious consumer, and the Health-oriented consumer. These consumer segments differed with respect to their importance ratings for fruit choice motives. Furthermore, the willingness to buy specific fruit innovations (i.e., genetically modified, functional food and convenience innovation) and the perceived product characteristics that influence this willingness differed across the segments. Our study could lead to more tailored marketing strategies aimed at increasing consumer acceptance of fruit product innovations based on consumer segmentation.