Production of single cell protein (SCP) from natural gas in a one liter bubble column reactor and optimization of the process parameters were investigated. The medium specifications, nitrogen sources, initial inoculum volume, and inlet ratio of gas to air were considered as process parameters to be optimized. The optimum condition for highest biomass production in which the maximum quantity of protein was obtained, were the use of a certain carbon-less salt broth utilizable with methane (named as Methane Salt Broth/MSB) and sodium nitrate as medium and nitrogen source respectively. Also, 7%(v/v) inoculation size, and an inlet gas mixture of 60/40 natural gas/air were determined as the effective inoculation and appropriate volume configuration of inlet gases. Protein production in optimum condition was 69.3 %( w/w) of biomass in dry basis which its structural amino acids can be in comparable with other nutrient sources. An average amount of 10 g RNA out of 100 g of cellular protein [or 6 %(w/w) RNA in whole biomass] was extracted from the biomass which is extremely near to the possible minimum of RNA distribution among bacteria. Heat shock treatment was applied for reducing the RNA in the biomass bulk. Heat Treatment at 60 to 65°C for 10 to 20 min provided the best RNA reduction results (around 1 gram in 100 grams of protein). Regarding the structural amino acids and RNA content, the properties of single cell protein resulted in this experimental work, were in a frame which it could be consumed safely.