Profitability of an integrated food bioprocessing industry (IFBI) depends on consumer trust and sustainability. Food quality and safety are central to ensuring consumer health. Hence, this chapter explored the concepts of food quality, safety, and sustainability in an IFBI. Legal requirements and international standards ensure uniformity of standards of quality control and safety in an IFBI. Moreover, following these standards ensure global acceptability of food products. Therefore, an IFBI must implement quality management system and food safety management system in its processing facility and supply chain. Control of microorganisms, enzymatic activity, pests, and physical damage can prevent quality and safety deterioration of foods. The major threats to food safety are pathogenic microorganisms and toxicants. Implementation of a comprehensive quality control and safety strategy encompasses all the components of industry including layout of processing facility, inspection of raw ingredients, preliminary processing, further processing, quality assurance (QA), quality control (QC), labelling, storage, and transportation. Since workers are the main handlers of food products, so they must be trained for food safety, quality control, and personal hygiene. The IFBI must ensure proper cleaning and disinfection system, waste disposal system, effective pest control system. Many novel food processing technologies have shown promise to control microbial deterioration, however, a combination of various methods can be more beneficial. This chapter will not only serve food producers as a basic guideline for establishing a comprehensive quality control and food safety system, but also provide guidance to regulators to device an effect food safety regulation.