A sediment core encompassing the last 2000 years was extracted from Lake Laja, Chile, (36°54′S, 71°05′W) using an Uwitec drilling platform. The sediment was subsampled for loss on ignition, nutrients, biogenic silica, and biological proxies (diatoms, chironomids, pollen). The sedimentary profile was characterized by several coarse volcanic layers. Loss on ignition, nutrients, and biogenic silica showed an increasing trend that suggests a recent shift to a higher trophic status. Diatom assemblages also suggested higher nutrient content with increased abundances of Aulacoseira granulata, A. distans, and Asterionella formosa. At the same time, a marked change in the benthic and facultative planktonic taxa may be associated with cooling. This period of change coincides with the European Little Ice Age (LIA). The chironomid profile showed four key zones distinguished largely by changes in the abundance of Tanytarsini, Parachironomus, and Macropelopia. Like diatoms, chironomids also seemed to reflect a shift to higher trophic conditions in the upper part reflected by increasing abundance of taxa such as Tribelos/Phaenopsectra, Cricotopus/Orthocladius, and Ablabesmyia. The most striking feature in the chironomid assemblage is the abundance of Podonominae, Parapsectrocladius, and Limnophyes/Compterosmittia, which could be associated with a cold-dry period between 1500 and 1900 AD in Lake Laja (the period of the European LIA). Pollen assemblages indicated fluctuations in humidity through changes in Nothofagus dombeyi-type, Poaceae, and Ephedra, and we inferred a strong human impact over the last 100 years from the appearance of Plantago and increased levels of Poaceae and Asteraceae subf. Cichorioidae. Finally, the three proxies showed the occurrence of a cold-dry event in Lake Laja (~1550–1900 AD), which roughly coincides with the European LIA. However the data from this research, does not prove neither rejects the existence of the occurrence of the MWP in the central Andes.