This study was designed to have the absolute definition of ‘one apple to one puree’, which gave a first insight into the impacts of fruit inter-variability (between varieties) and intra-variability (between individual fruits) on the quality of processed purees. Both the inter-variability of apple varieties and the intra-variability of single apples induced intensive changes of appearance, chemical and textural properties of their corresponding microwave-cooked purees. The intra-variability of cooked purees was different according to apple cultivars. Some strong correlations of visible-near infrared (VIS-NIR) spectra were observed between fresh and cooked apples, particularly in the regions 665–685 nm and 1125–1400 nm. These correlations allowed then the indirect predictions of puree color (a* and b*, RPD ≧ 2.1), viscosity (RPD ≧ 2.3), soluble solids content (SSC, RPD = 2.1), titratable acidity (RPD = 2.8), and pH (RPD = 2.5) from the non-destructive acquired VIS-NIR spectra of raw apples.