Synchrony in the second modes of an empirical orthogonal function (EOF) analysis of global physical and biological properties is described for the 1993–2010 time period. High correlations are found between the El Niño Modoki index and principal component time series of sea surface temperature, sea surface salinity, photosynthetically active radiation, precipitation, surface currents, surface chlorophyll concentration, and equatorial temperature profiles. Spatial patterns indicate that the second mode is also associated with the North Pacific Gyre Oscillation (NPGO). Biological changes during traditional El Niños (first EOF mode) have been explained on the basis of strong and coherent variations in thermocline depth, wind-driven upwelling and light, but changes associated with the second mode are more subtle and complex. Equatorial temperature profiles indicate that the warming is confined to the mixed layer and that changes in thermocline depth are small. The biological changes associated with the second mode may be driven by a combination of weak perturbations to vertical nutrient supply and the strength of subtropical gyres. In the western tropical Pacific, the site of some of the strongest perturbations, the biological changes can be associated with the occurrence and thickness of barrier layers and to island effects downstream of the Kiribati Islands. Globally integrated impacts of the second mode are much weaker than those associated with the traditional ENSO. During the positive phase, chlorophyll is strongly enhanced in the tropics and weakly enhanced at the global scale in sharp contrast to traditional El Niño effects. The analysis improves our understanding of global-scale physical and biological coupling associated with the so-called El Niño Modoki and the NPGO.