Archaeological bone artifacts are found in different locations in Egypt, and they represent multiple values that should be preserved from different deterioration factors. Iron contamination is considered one of the most aspects of deterioration for bones extracted from excavation areas. This study aims to make an integrated study for the first time on the formation of iron rust stain on archaeological bones, explain the aspects and mechanism of its deterioration, explain traditional and advanced techniques of cleaning used for stain removal, and presents the analysis and investigations used to explain the deterioration or evaluate the materials and methods used in this process. The nature and formation of iron stain and its effect on archaeological bone components were explained. The cleaning techniques (mechanical, chemical, laser, and plasma) for removing it were discussed. Some analyses and investigations [such as different types of microscopes, X-ray fluorescence, Atomic absorption, Fourier Transform Infrared (FTIR) spectroscopy, etc.] that can be used in this process were mentioned. The results confirmed that iron is present within sediments can lead to the breakdown of collagen. It can cause an increase in the porosity of bone artifacts. Hydroxyapatite can undergo alterations such as ionic exchange, cationic exchange, and substitution of phosphate with carbonate. All cleaning techniques have many advantages and some disadvantages. The choice of method for cleaning of iron rust stain depends on the condition and size of the bone piece, and on the thickness and nature of the iron stain.