The main threat to A. pallidipectoris is habitat degradation and loss. The Gran Chaco region and especially the more arid part, the Dry Chaco, is highly appreciated for cattle-farming (Paraguay, Bolivia) and soy bean culture (Argentina). In the last decade the deforestation rates of the arid Chaco have increased dramatically. The main areas of deforestation in Paraguay and Argentina match closely the distribution map of the species (compare Hansen et al. 2013).
In the main area of occurrence of A. pallidipectoris in Paraguay, the Department Boquerón, a portion of 1.9 million ha (21.7 % of the total surface) received permits to be cleared between 2003 and 2012, of which 78.6% (1.6 million ha and 17.0% of the total surface) had been permitted in the last six years (2007-2012) (Torres 2008, Barrios Kuck and Torres 2013). It is expected that in the Paraguayan Chaco all suitable land (land not located within the national protected area system, or reserved for indigenous communities, or held as private protected areas) will have been transformed for cattle production by 2025 (Yanosky 2013). This trend is not any better in Argentina with an increase of the deforestation rate in the Chaco by 439% from 2011 to 2012 (43,717 to 235,601 ha), keeping nearly the high level also in 2013 (Vinke et al. 2011, Rodas et al. 2012, Palacios et al. 2013, Cardozo et al. 2014).
In contrast to Acanthochelys macrocephala, which seems to be adapting to the altered landscape by opportunistically utilizing artificial cattle ponds (Vinke and Vinke 2001, 2008), this development is fatal for A. pallidipectoris due to its dependence of the above described microhabitat. For the cattle farmers the clay soil of those lowland depressions is of extreme high value and therefore this habitat type is widely destroyed by digging it out either directly as deep water reservoirs for cattle or by using the soil to build high tanks for the same function. Both of these destroy the habitat for A. pallidipectoris. The clay soil is also excavated for use in road building.
In Argentina the greatest threat is due to extensive habitat loss through intensive monocultures of soybean, especially in the provinces of Chaco, Formosa, Santiago del Estero, northwestern Santa Fe and northeastern Salta. This monoculture leads to a serious risk regarding the stability of the complete Chaco ecosystem, and therefore to the populations of A. pallidipectoris, which only is found within the few isolated remains of the native Chaco vegetation. A survey of the region of the Chaco of the province Salta in 2009 showed the huge devastation (E. Richard pers. obs.; Vinke et al. 2011), leaving the native fauna without suitable habitat.
In addition in Paraguay, competition with A. macrocephala and Caiman yacare, which have both migrated into the dry Chaco following the habitat modification of cattle farming and cattle ponds, are apparent threats in places where more water is available (Vinke and Vinke 2008). Finally, data suggest that changing climate regimes causing drought and abnormally low temperatures in winter and extremely high temperatures in spring and summer are likely to become a threat in the future (i.e. the 2007 winter was the coldest on record in South America, and the drought in 2008-2009 lasted for 16 months in the Chaco (T. Vinke and S. Vinke pers. obs.).
Although the species is legally protected in all of its range countries, more or less continuous offers of sale are observed in the international Internet trade. However, it is not known how many animals are collected illegally, nor from which countries or sites (Vinke et al. 2011), but the effects on wild populations are probably significant.