Initial evaluations of the System of Rice Intensification in India and elsewhere focused mainly on its impacts on yield and income, and usually covered just one or two seasons. Researchers at the ICAR-Indian Institute of Rice Research have conducted a more comprehensive evaluation of SRI methods over six years (six wet and six dry seasons), comparing them with three alternatives: modified, partially mechanized SRI (MSRI) to reduce labor requirements; direct-seeded rice (DSR) as an alternative method for growing rice; and conventional transplanting of rice with flooding of fields (CTF). Grain yield with SRI methods was found to be about 50% higher than with CTF (6.35 t ha−1 vs. 4.27 t ha−1), while the MSRI yield was essentially the same (6.34 t ha−1), 16% more than with DSR (5.45 t ha−1). Water productivity with SRI methods was 5.32–6.85 kg ha-mm−1, followed by 4.14–5.72 kg ha-mm−1 for MSRI, 5.06–5.11 kg ha-mm−1 for DSR, and 3.52–4.56 kg ha-mm−1 for CTF. In comparison with CTF, SRI methods significantly enhanced soil microbial populations over time: bacteria by 12%, fungi by 8%, and actinomycetes by 20%. Biological activity in the rhizosphere was also higher as indicated by 8.5% greater dehydrogenase and 16% more FDA enzymes in soil under SRI management. Similarly, an indicator of soil organic matter, glucosidase activity, was 78% higher compared to CTF. SRI enhanced the relative abundance of beneficial microbial-feeding nematodes by 7.5% compared to CTF, while that of plant-pathogenic nematodes was 7.5% lower under SRI. Relative to conventional methods, SRI management reduced GHG emissions by 21%, while DSR reduced them by 23%, and MSRI by 13%, compared to standard rice-growing practice. Economic analysis showed both gross and net economic returns to be higher with SRI than with the other management systems evaluated. While the six-year study documented many advantages of SRI crop management, it also showed that MSRI is a promising adaptation that provides similar benefits but with lower labor requirements.