Fruit quality is an important aspect in determining the consumer preference in the supply chain. Thermal imaging was used to determine different pineapple varieties according to the physicochemical changes of the fruit by means of the deep learning method. Deep learning has gained attention in fruit classification and recognition in unimodal processing. This paper proposes a multimodal data fusion framework for the determination of pineapple quality using deep learning methods based on the feature extraction acquired from thermal imaging. Feature extraction was selected from the thermal images that provided a correlation with the quality attributes of the fruit in developing the deep learning models. Three different types of deep learning architectures, including ResNet, VGG16, and InceptionV3, were built to develop the multimodal data fusion framework for the classification of pineapple varieties based on the concatenation of multiple features extracted by the robust networks. The multimodal data fusion coupled with powerful convolutional neural network architectures can remarkably distinguish different pineapple varieties. The proposed multimodal data fusion framework provides a reliable determination of fruit quality that can improve the recognition accuracy and the model performance up to 0.9687. The effectiveness of multimodal deep learning data fusion and thermal imaging has huge potential in monitoring the real-time determination of physicochemical changes of fruit.