Reducing food wastage is one of the challenges in achieving global food security and transforming current food systems. Since human nutrition is closely dependent on cereal production, research was undertaken aimed at understanding the food losses in the baking and confectionery industry (BCI) in Poland, in particular at determining the volume, reasons and ways of reducing losses, identifying possibly all of the reasons for losses in BCI using the Ishikawa 5M + 1E diagram and determining the level of significance and probability of risk of food losses in the analysed sector. Two research methods were used. Quantitative data were collected using the mass balance method from five businesses that served as case studies. Qualitative data were collected through individual in-depth interviews with 17 industry experts. The companies’ average daily losses ranged from 0.8 to 6.4 tons, representing 9.7 to 14.4% of production volume, including 10.4–13.4% of bread losses and 6.8–24.4% of fresh pastry losses. The highest losses were generated by transport departments and these were exclusively retail returns. Following the Ishikawa concept, 31 primary and 94 secondary reasons for food losses were identified. Using the probability of loss risk, a toolkit for loss prevention and mitigation across all departments within businesses (raw materials magazine, production section, final product magazine and final product transport) and a set of horizontal tools were identified, including specialised training for employees and activities in several areas, e.g., technical status and production technology, organisation and planning, logistics and sales and cooperation with retail. This study, conducted in Poland, offers valuable results for developing programmes and strategies to prevent and manage food losses in BCI. Many of the solutions proposed in both toolkits can bring economic benefits without involving additional high costs.