The importance of biogas in the energy mix in Poland and Latvia is very low. In Poland, 306 million m3 of biogas is produced annually, and in Latvia, 56 million m3. The share of energy from agricultural biogas in Latvia is 1.6%, and in Poland, only 0.12%. This study analyzed the impact of the structure on CO2 emissions from agricultural biogas production in Latvia and Poland. The emission was determined in accordance with the EU directive. The structure of substrates was dominated by those from the second generation, i.e., manure and food waste. In Latvia, it was 70%, and in Poland, 78%. The manure share was 45% and 24%, respectively. The anaerobic digestion of manure guarantees high GHG savings thanks to the avoided emissions from the traditional storage and management of raw manure as organic fertilizer. The level of emissions from the production of agricultural biogas was calculated for the variant with the use of closed digestate tanks, and it was about 10–11 g CO2/MJ, which is comparable to the emissions from solar photovoltaic sources. When using open tanks, the emission level was twice as high, but it was still many times less than from the Polish or Latvian energy mix. Such a low level of emissions resulted from the high share of manure. The level of emission reduction reached 90% compared to fossil fuels. The use of second-generation feedstock in biogas production provides environmental benefits. Therefore, if wastes are used in biogas generation, and the influence on the local environment and overall GHG emissions is positive, authorities should support such activity.