An evaluation was conducted in eastern India over three years, 2005–2007, to compare the performance of certain System of Rice Intensification (SRI) practices: transplanting single, young (10-day-old) seedlings in a square pattern; no continuous flooding; and use of a mechanical weeder – with those currently endorsed by the Central Rice Research Institute of India, referred to here as recommended management practices (RMP). All plots received the same fertilization, a combination of organic and inorganic nutrients, and the SRI spacing used was 20% less than usually recommended. Accordingly, the results reported here are designated as a modification of SRI recommendations (SRIm). The objective of this research was to understand the benefits in terms of yield and other physiological parameters, if any, from using most if not all recommended SRI practices compared to RMP. These selected SRI practices out-yielded RMP by 42%, with the higher yield associated with various phenotypical alterations, which are reported here. Significant measurable changes were observed in physiological processes and plant characteristics, such as longer panicles, more grains panicle−1 and higher % of grain-filling. The decreased plant density with SRIm management was compensated for by increased per-plant productivity. SRIm hills with single plants were found to have deeper and better-distributed root systems, higher xylem exudation rates, more open plant architecture with more erect and larger leaves, and more tillers than did RMP hills having multiple plants. Due to the reduction in number of hills m−2 in SRIm plots compared to RMP, no significant difference was found in root dry weight or leaf number, tillers or panicle number on an area basis. Nevertheless, in spite of SRIm having fewer hills and fewer tillers per unit area, the leaf area index (LAI) with SRIm practice was greater due to larger leaves. These together with altered plant architecture, contributed to more light interception by SRIm plants. The higher leaf chlorophyll content at ripening stage reflected delayed senescence and the greater fluorescence efficiency (Fv/Fm and ФPS II) associated with SRIm practices contributed to more efficient utilization of light and a higher rate of photosynthesis, which was probably responsible for the observed increase in grain filling and heavier grains compared to RMP plants. The higher photosynthesis rate coupled with lower transpiration in SRIm plants indicated that they were using water more efficiently than did RMP plants. The latter produced 1.6 μ mol CO2 fixed per m mol water transpired, compared to 3.6 μ mol CO2 in SRIm plants.