Over the centuries, honey is known for its superior usage in culinary, and for its rich nutrition and therapeutic values which are scientifically proven in the medical field. The chemical composition of honey varies depending on its botanical sources and environment. Therefore, the nutrition content in honey is highly likely to be affected by contaminants, such as heavy metals and pesticides. To ensure the quality of honey, parameters such as the heavy metal content should be within the safe range of total standard mineral and trace elements as defined by the International Food Standard (Codex Alimentarius), and pesticides should not be present at all. The high concentration of heavy metal and pesticides not only deteriorates the quality and quantity of honey, but also causes harm to the bee colony itself. In the agriculture sector, the excessive usage of pesticides and fertilizer negatively impacts the overall honey production process. Bees, a pollinating agent, bring the polluted nectar back to their beehives, eventually contaminating the honey and depreciating its value. Hence, this article will comprehensively review the activities that contribute to heavy metal and pesticide contamination, the interactions of bees as a pollinating agent, the impact of the pollutant to the colonies, and subsequently to the honey production.