<p>Modern agricultural practices and dairy processing are associated with a higher risk of food safety threats originating from a variety of physical, chemical, and microbiological hazards. These include the use of various chemicals, including pesticides, herbicides, fertilizers, and cleaning agents, resulting in an unhealthy accumulation of residues on food, leading to chronic diseases, illnesses due to toxicity, or diseases caused by food. Furthermore, microbiological contaminants (pathogenic bacteria, viruses, and fungi) accumulate at different stages of agriculture and dairy processing responsible for a considerable share of the global foodborne disease burden. The aim of this review is to analyze from critical perspectives the chemical and microbiological contaminants of agriculture and dairy processing, their sources, pathways, and impact on humans. It reviews current food safety risk management practices, highlighting shortcomings and areas for improvement. The main strengths show that antibiotics, disinfectants, and heavy chemical residues are not only hazardous for food safety purposes, but they can also degrade product quality characteristics. Effective monitoring systems and coordinated risk reduction strategies are required to respond to such hazards, whose multifaceted nature complicates management. This review highlights the growing need for the implementation of advanced technologies, novel preventive interventions, and integrated food safety systems. Leading on from these findings, further interventions are needed that are cost-effective, scalable, and evidence-based, reducing the risk of contamination and ultimately improving health outcomes and sustainable food production systems.</p>