Conservation tillage practices, such as reduced tillage and no-tillage, have recently garnered significant attention as core elements of the regenerative agriculture and carbon farming concepts. By minimizing mechanical soil disturbance, these practices preserve soil carbon and facilitate CO2 fixation in the soil. Despite the widely acknowledged benefits, many farmers still approach no-tillage with skepticism. Their primary concerns are weed management and soil compaction. While weeds can be effectively controlled with the deployment of integrated weed management strategies, urgent soil compaction problems can be rapidly resolved only with mechanical interventions. That is why many no-till farmers resort to occasional heavy tillage, in a scheme characterized as rotational tillage, inadvertently sacrificing their regenerative assets in soil carbon. This is also a pivotal issue within carbon farming: the fate of soil carbon at the end of a compliant scheme focused on carbon fixation. The present study explores data of soil organic matter (SOM), soil penetration resistance (PR), and dry bulk density (DBD) from the initial, six-year period of a long-term tillage experiment in Greece. During that period, modifications to the experimental design allowed diverse combinations of five tillage methods (conventional tillage, 3 reduced tillage methods, and no-tillage). The findings indeed underscore the farmers’ concerns about soil compaction. High levels of PR and DBD were observed even at the topsoil layer of the no-tillage (NT). Conventional, moldboard plowing (MP) or reduced, chisel plowing (CP) applied after four years of uninterrupted no-tillage ameliorated most of the soil compaction; however, at the same time, this induced unfavorable consequences for SOM. In contrast, NT applied permanently for six years resulted in a substantial enhancement in SOM that reached 2.24%, for a sampling depth 0–0.30 m compared to 1.54% for permanent MP. When no-tillage was rotated with plowing in the fifth year, almost 50% of the sequestered carbon was lost and the SOM dropped to 1.87%. Nevertheless, the amount of SOM observed at the deeper 0.15–0.30 m layer was greater compared to permanent NT. This suggests that while plowing induced some loss of SOM, it also facilitated the uniform distribution into the soil profile, in contrast with the accumulation in the topsoil at prolonged NT. The permanent CP method and the NT/CP rotation provided comparative outcomes in terms of both soil compaction and soil carbon sequestration with the rotational NT/MP scheme, while all the other tillage combinations were inferior.