Introduction Eosin stain is a commonly used histological dye that selectively binds to acidic structures in cells, imparting a color between pink and red. Eosin stain can be harmful due to its chemical composition. Inhaling eosin stain in powder form or as aerosolized droplets can cause irritation in the respiratory tract. To overcome the toxic effects of eosin, many naturally available organic substitutes have been tested in histopathology laboratories, including rose extract, beetroot stain, and curcumin. These natural stain alternatives provide effective staining of tissue while ensuring minimal risk to laboratory personnel. Aim The study was conducted to evaluate the efficacy of food coloring agents over eosin stain in histopathological investigations. Materials and method The study was carried out in Kalinga Institute of Dental Sciences, Kalinga Institute of Industrial Technology (KIIT) (Deemed to be University), Bhubaneswar, India. The sample size comprised 30 oral mucosal lesion blocks. After the preparation of four micron thick sections from each block, one was stained with hematoxylin and eosin (H&E) stain and the other with a food coloring agent. Sections were kept in food color stain for three minutes. Next, the sections were dehydrated, cleared, and mounted in dibutylphthalate polystyrene xylene (DPX). To evaluate the staining with H&E and food color, each section was scored 0 for inadequate staining, one for adequate, and two for excellent staining. The tissue components stained for the study were red blood cells (RBCs), collagen fibers, muscle fibers, epithelium overall, basement membrane, cell membrane, desmosomes, keratin, cytoplasm, and nuclei. Kolmogorov-Smirnov tests were used to calculate the inferential statistics for the different variables between the groups. The distribution of the study sample was found to be not normal; therefore, a nonparametric test of significance was applied. Results All the tissue components showed excellent staining by H&E (score 2). Among the tissue components, in most of the samples, keratin, cytoplasm, and RBCs showed excellent staining (score 2) on par with the H&E stain. Other tissue components showed no staining (score 0) to adequate staining (score 1). The basement membrane and cell membrane staining were not adequate (score 0). The nuclear staining by hematoxylin was unaffected by food color and was on par with normal H&E staining. Conclusion We conclude that tomato red food color, which is non-toxic, safe for the health of laboratory personnel, easy to dispose of, and environmentally friendly, could be used as a replacement for eosin in the routine H&E techniques. Our observations could be strengthened by increasing the sample sizes and modifying the stain preparation to ensure positive staining of all tissue components, thereby enhancing the results.