We investigate the spatio-temporal variability of normalized difference vegetation index (NDVI) associated with deforestation in four zones in southeastern Peru (Madre de Dios Region): (1) an area comprising part of the Tahuamanu province (mainly, but it also comprises a small part of Tambopata province), (2) a part of the Tahuamanu watershed, (3) surrounding areas of Iñapari and Iberia towns, and (4) another area in the Iñapari district which we labelled as Iñapari-B. We have utilized three statistical tools: the empirical orthogonal function (EOF), Fourier analysis, and wavelet analysis. EOF was used to obtain the maximum variability of the NDVI-anomaly spatial patterns and also their associated temporal variability as time series. Fourier analysis was used to determine the periodicities on the EOF pattern and associated them to deforestation in the region. Wavelet analysis was used to detect the maximum variability of the phenomena and to portray their statistical significance along the period of study and so identify when the maxima happen. From the results obtained, in Zone I, we have found a 2-month deforestation periodicity with major peaks in 2004 and 2009; in Zone II, the periodicity is about 1.8 months, with a maximum peak in 2009; in Zone III, the periodicity is 2.4 months with the highest peak in 2009; in Zone IV, the high-frequency periodicity is about 2.8 months with the main peaks in 2000, 2003, and 2004.