The adoption of anaerobic soil disinfestation (ASD), a biologically-based method for the management of soilborne pests and pathogens at the commercial scale strictly depends on the availability of effective and low-cost sources of carbon (C). A three-phase pot study was conducted to evaluate the performance of twelve cover crop species as alternative sources of C in comparison to molasses. Buckwheat produced the greatest above-ground and total plant dry biomass and accumulated the largest amount of total C. In the second phase, simulating the application of ASD in a pot-in-pot system, molasses-amended soil achieved substantially higher levels of anaerobicity and lowered soil pH at 3 and 7 days after treatment application compared to soil amended with the cover crops tested. In the third phase of the study, after the ASD simulation, lettuce was planted to assess the impact of cover crops and molasses-based ASD on lettuce yield and quality. The treatments had limited effects on lettuce plant growth and quality as none of the treatments caused plant stunting or phytotoxicity. Tested cover crop species and molasses had a significant impact on the availability of macro and micro-elements in the soil, which in turn influenced the uptake of minerals in lettuce. Fast-growing cover crops like buckwheat or oat, capable of accumulating high levels of C in a relatively short time, may represent a viable alternative to substitute or be combined with standard C sources like molasses, which could provide an on-farm C source and reduce cost of application. Further research is needed to assess the performance of cover crops at the field scale and verify their decomposability and efficacy in managing soil-borne pests and pathogens.