Diatom records from the East Pisco Basin (EPB) of southern Peru and offshore Ocean Drilling Program (ODP) Hole 682 A reveal stepwise increases in the primary productivity of the Humboldt Current during the middle and late Miocene. Although diatoms are present back through the late middle Eocene, successively enhanced diatom production occurs during the Miocene in four steps. The first step between 14.2 and 13.8 Ma marks the onset of diatom deposition in the Pisco-0 sequence. A second step at ∼12.9 Ma coincides with a major drop in global sea level during which diatom deposition ceased in the EPB but continued in ODP 682 A as well as in Chile, Ecuador, and Colombia. Beginning at 10.4 to 10.0 Ma, a major increase in diatom sedimentation rates in both the EPB and in ODP 682 A signals an abrupt intensification of the Humboldt Current productivity, which may be related to the closure of the Central American Seaway to deeper water circulation. A fourth step coincides with the transgressive deposition of the diatom-rich Pisco-2 sequence at 8.4 Ma and is enhanced by the onset of the global Late Miocene Biogenic Bloom (8.0–4.5 Ma). Between 7 and 6 Ma, common subtropical diatoms in ODP 682 A contrast with high diatom deposition rates in the EPB, suggesting variable El Niño-La Niña conditions. During this time, fossil vegetation evidence from southern Peru supports the presence of seasonal periods of enhanced rainfall typical of El Niño conditions. The Miocene trend of increasing sea mammal diversity in the EPB parallels these steps, further supporting stepwise enhancement of primary productivity in the Humboldt Current during the Miocene.