Encapsulation of methane producing bacteria was performed to enhance the rate of biogas production, using natural as well as synthetic membranes. A one-step liquid-droplet-forming method was employed for the natural membrane, resulting in spherical capsules with an average diameter and a membrane thickness of 4.3 and 0.2 mm, respectively. The capsules were made from alginate, with chitosan or Ca2+ as counter-ions, with addition of carboxymethylcellulose (CMC). For synthetic capsules, the Durapore® membrane (hydrophilic PVDF), with a pore size of 0.1 µm, was used for capsules of the sizes 3×3 and 3×6 cm, holding the bacteria. During the digesting process the dissolved substrates penetrated through the capsule membranes, and biogas developed inside the capsules, escaping by diffusion. The results indicate that encapsulation is a promising method of digestion, with a high density of anaerobic bacteria. The method holds a considerable potential for further development of membranes and their applications.