The use of Microfiltered Water Dispensers (MWDs) is increasing in offices, companies, or commercial facilities, as a response to plastic pollution. Despite their widespread use, poor data are available about the water quality and pathogens developed. Starting from a high contamination found in MWDs, a Water Safety Plan (WSP) was implemented on 57 MWDs to improve the water quality. To assess the effectiveness of WSP during the period 2017–2021, the environmental monitoring of heterotrophic plate counts (HPCs) at 36 °C and 22 °C, Enterococcus spp., Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, and Clostridium perfringens, as prescribed by Italian regulation for drinking water, was conducted. A high level of HPCs at both temperatures was observed, over the regulation limit; contrarily, the pathogenic bacteria were absent. The contamination found was studied with respect to the temperature threshold of 25 °C, suggested by directives. No significant differences were found between samples above and below the threshold, while a significant decrease over the years was observed for HPCs at 36 °C (p = 0.0000000001) and 22 °C (p = 0.000006). The WSP implementation resulted in a 43.09% decrease for HPCs at 36 °C and a 24.26% decrease for HPCs at 22 °C. Moreover, during the SARS-CoV-2 pandemic, the WSP contributed to limit the microbial contamination, preserving the MWDs’ functionality and hygienic conditions and the drinking water quality.