The organizations of horticultural producers and, particularly, those that deal with extremely perishable endogenous fruits, such as peaches and cherries, have a greater need to optimize production flows and processes. A particularity of the horticultural industry is the short shelf life of raw materials and the seasonality of products. In this paper, optimization techniques are used to improve the production flows and the management of cold storage and distribution in a fruit central. The application of Lean tools allowed reducing the cycle time by 4.37 min and the lead time by 7.10 min of the whole process, i.e., a reduction of 35.5% and 10.6% of the cycle time and lead time, respectively, excluding the cold conservation operation. The study shows that it is possible to reduce, or even eliminate, waste throughout the process, reduce unnecessary movement, adapt the layout, maximize workspace, and level stocks, as well as greater supplier involvement in a continuous improvement approach. This approach can be outlined as a good practice for the optimization of productive flows and management logistics that may benefit productivity, energy efficiency, human resources distribution, food quality, and reduce food waste.