The study of microbial populations of biohydrometallurgic processes is generally more focused on the solutions involved than on the minerals. This is mainly due to complexity and costs associated with taking mineral samples during the leaching cycle. The present study compares the microorganisms in the solutions and the minerals in 1 m test columns and in samples taken from two strips of an industrial heap from the Escondida Copper Mine in Chile. The column test was carried out in six 1 m columns that were operated with similar parameters than the industrial heap. The industrial heap is divided into strips, and samples were collected from Strip 1 (after the end of the operation) and from Strip 9 (during the irrigation period). To analyze the bacterial population Real-Time PCR and CARD-FISH techniques were used. From the results of the column leaching tests a slightly greater cellular density was observed for the mineral than the solution, when the total bacterial count was considered. In both types of samples the predominant microorganisms were Acidithiobacillus thiooxidans, Acidithiobacillus ferrooxidans D2 and Leptospirillum ferriphilum. In the samples from the industrial heap A. ferrooxidans predominated at the start of operation and A.thiooxidans at the end of the leach cycle.