Egypt is encouraging micro-scale enterprises as proved to be one of the most important reasons of economic growth. Most of the annual milk production is processed in micro-scale dairy enterprises located in squatter areas with high health risks and negative environmental impact. The aim of this study was to assess the effectiveness of in-plant control measures in controlling lead and cadmium levels in dairy products from nine Egyptian micro-scale enterprises. The results revealed that white cheese enterprises had the highest mean lead and cadmium contents; both in their raw milk (0.712 and 0.134 mg/L, respectively) and final products (0.419 and 0.061 mg/kg). Higher compliance percentages were found with cadmium levels specified in the Egyptian standards than with lead levels and ranged from 59.4% in raw milk to 100% in dry milk for cadmium levels and from 8.3% in white cheese to 66.7% in ice cream for lead; moreover, none of the collected raw milk samples were complying with the lead levels. After implementation of in-plant control measures, lower lead levels were found in all samples with reduction percentages ranging from 35.2% in raw milk from the ice cream enterprises to 73.2% in yoghurt; moreover, higher percentages of samples complied with cadmium levels. This study highlights the urgent need for applying in-plant control measures to the Egyptian micro-scale dairy enterprises to improve both safety and quality of their products.