© 2016 Elsevier Ltd Nanomechanical properties of fruit determine macroscopic firmness. Young's modulus (YM) of apple tissue obtained by atomic force microscopy (AFM) at cellular level and its correlation with other macroscopic physical parameters are used to evaluate ripening when apples were stored at 25 °C during 40 days. The YM of the tissue decreased from 0.96 ± 0.42 MPa (first day) to 0.11 ± 0.06 MPa (last day). The best linear correlation of YM was obtained with firmness (F) which decreased from 21.15 ± 0.79 N to 12.74 ± 0.34 N. Also various physical parameters obtained as peel color difference (ΔE) from 57.80 ± 0.97 to 66.51 ± 0.71, environmental electron microscopy (ESEM) such as entropy: Ent (from 8.67 ± 0.12 to 9.60 ± 0.17) and fractal dimension: FD (from 2.67 ± 0.05 to 2.75 ± 0.03) changed as well. Significant correlations (P < 0.05) were found between YM, F, ΔE, Ent and FD using Pearson analysis. Predictive models to evaluate YM from F, ΔE, Ent, FD were obtained by multiple linear regression, R2 > 0.95 was found. Industrial relevance The study of the nanomechanical properties of fruit cells by AFM may provide insight into internally fruit properties and how changes in these properties over time influence the quality of the fruit. The determination of cell/tissue mechanics could be used to follow changes in the nanomechanical properties that occur during the processing and storage of climacteric fruits such as apples. The study of the nanomechanical properties of plant cells as well as their correlation with other useful food properties such as firmness, peel color and image texture could lead to a better understanding of the ripening process. Mathematical models to predict cell mechanical properties at the nanometric level through food quality parameters could be an innovation in food engineering and be a novel tool in evaluating the quality of apples. Benefits of the methods herein could be extended to address current issues, such as extending the storage life of other climacteric fruits and predicting nanostructural modifications to the cells when they are physically modified or chemically treated.