Lung and colon cancers are two of the most common causes of death and morbidity in humans. One of the most important aspects of appropriate treatment is the histopathological diagnosis of such cancers. As a result, the main goal of this study is to use a multi-input capsule network and digital histopathology images to build an enhanced computerized diagnosis system for detecting squamous cell carcinomas and adenocarcinomas of the lungs, as well as adenocarcinomas of the colon. Two convolutional layer blocks are used in the proposed multi-input capsule network. The CLB (Convolutional Layers Block) employs traditional convolutional layers, whereas the SCLB (Separable Convolutional Layers Block) employs separable convolutional layers. The CLB block takes unprocessed histopathology images as input, whereas the SCLB block takes uniquely pre-processed histopathological images. The pre-processing method uses color balancing, gamma correction, image sharpening, and multi-scale fusion as the major processes because histopathology slide images are typically red blue. All three channels (Red, Green, and Blue) are adequately compensated during the color balancing phase. The dual-input technique aids the model’s ability to learn features more effectively. On the benchmark LC25000 dataset, the empirical analysis indicates a significant improvement in classification results. The proposed model provides cutting-edge performance in all classes, with 99.58% overall accuracy for lung and colon abnormalities based on histopathological images.