The objective of this research was to evaluate the influence of procedures for hygienic milking and cleaning of dairy equipment and milk cooling tanks on the levels of total bacterial count (TBC). Mixed-effect models were used in order to model the structure of dependence between and within dairy farms. To this end, four bulk samples of milk were collected from each tank in eight properties for TBC analysis, employing the flow cytometry method. A questionnaire was applied in each property to assess the current situation of milking procedures on each production system that took part on this research, followed by training of employees in good agricultural practices in the production of milk and monitoring of the TBC measurements. Analysis of longitudinal data was the method employed, which focused on random effects models. The results showed that the handling procedures for milking and the cleanliness of the cooling tanks contributed to a further reduction in the levels of total bacterial count in raw milk cooling tanks.