Methane is the second highest contributor to the greenhouse effect. Its global warming potential is 37 times that of CO2. Flaring-associated natural gas from remote oil reservoirs is currently the only economical alternative. Gas-to-liquid (GtL) technologies first convert natural gas into syngas, then it into liquids such as methanol, Fischer−Tropsch fuels or dimethyl ether. However, studies on the influence of feedstock composition are sparse, which also poses technical design challenges. Here, we examine the techno-economic analysis of a micro-refinery unit (MRU) that partially oxidizes methane-rich feedstocks and polymerizes the syngas formed via Fischer−Tropsch reaction. We consider three methane-containing waste gases: natural gas, biogas, and landfill gas. The FT fuel selling price is critical for the economy of the unit. A Monte Carlo simulation assesses the influence of the composition on the final product quantity as well as on the capital and operative expenses. The Aspen Plus simulation and Python calculate the net present value and payback time of the MRU for different price scenarios. The CO2 content in biogas and landfill gas limit the CO/H2 ratio to 1.3 and 0.9, respectively, which increases the olefins content of the final product. Compressors are the main source of capital cost while the labor cost represents 20−25% of the variable cost. An analysis of the impact of the plant dimension demonstrated that the higher number represents a favorable business model for this unit. A minimal production of 7,300,000 kg y−1 is required for MRU to have a positive net present value after 10 years when natural gas is the feedstock.