Low carbon fuel and waste management policies at the federal and state levels have catalyzed the construction of California's wet anaerobic digestion (AD) facilities. Wet ADs can digest food waste and dairy manure to produce compressed natural gas (CNG) for natural gas vehicles or electricity for electric vehicles (EVs). Carbon capture and sequestration (CCS) of CO(2) generated from AD reduces the fuel carbon intensity by carbon removal in addition to avoided methane emissions. Using a combined lifecycle and techno-economic analysis, we determine the most cost-effective design under current and forthcoming federal and state low carbon fuel policies. Under many scenarios, designs that convert biogas to electricity for EVs (Biogas to EV) are favored; however, CCS is only cost-effective in these systems with policy incentives that exceed $200/tonne of CO(2) captured. Adding CCS to CNG-producing systems (Biogas to CNG) only requires a single unit operation to prepare the CO(2) for sequestration, with a sequestration cost of $34/tonne. When maximizing negative emissions is the goal, incentives are needed to either (1) fund CCS with Biogas to EV designs or (2) favor CNG over electricity production from wet AD facilities.