Increasing biogas production in the Three Seas Initiative countries (3SI) is a good way to reduce greenhouse gas emissions and to increase energy self-sufficiency by replacing some of the fossil energy sources. An assessment of the biogas production potential carried out for the 3SI at the NUTS 1 and NUTS 2 level shows that the potential of this energy carrier was stable for the period (from 2010–2021). The results showed that it can cover from approximately 10% (Hungary, Slovakia) to more than 34% (Estonia, Slovenia) of natural gas consumption; moreover, there is strong variation in the value of potential at the regional level (NUTS 2) in most of the countries studied. The biogas production forecast was carried out with the ARIMA model using four regressors, which are GDP, biogas potential utilisation, natural gas consumption and investments in RES (renewable energy sources) infrastructure, including changes in the EU energy policy after 24 February 2022. In the most promising scenario (four regressors), the results obtained for the period from 2022–2030 predict a rapid increase in biogas production in the 3SI countries, from 32.4 ± 11.3% for the Czech Republic to 138.7 ± 27.5% for Estonia (relative to 2021). However, in the case of six countries (Bulgaria, Lithuania, Hungary, Austria, Poland and Romania) the utilisation of 50% of the potential will most likely occur in the fifth decade of the 21st century. The above results differ significantly for those obtained for three regressors, where the highest rise is predicted for Bulgaria at 33.5 ± 16.1% and the lowest for Slovenia, at only 2.8 ± 14.4% (relative to 2021).