Aims An attempt was made to optimize a new protocol for isolation of pure metagenomic DNA from soil samples. Methods and Results Various chemicals (FeCl3, MgCl2, CaCl2 and activated charcoal) were tested for their efficacy in isolation of metagenomic DNA from different soil and compost samples. Among these trials, charcoal and MgCl2 when used in combination yielded highly pure DNA free from humic acids and other contaminants. The DNA extracted with the optimized protocol was readily digested, amplified and cloned. Moreover, compared with a well-established commercial DNA isolation kit (UltraClean (TM) Soil DNA Isolation Kit), our method for DNA isolation was found to be economical. This demonstrated that the method developed can be applied to a wide variety of soil samples and allows handling of multiple samples at a given time. Conclusions The optimized protocol developed has successfully yielded pure metagenomic DNA amenable to biotechnological manipulations. Significance and Impact of the Study A user-friendly and economical protocol for isolation of DNA from soil and compost samples has been developed.