It excavates deep burrows in thick guano for nesting, but may also burrow in sandy soils or use natural rock crevices. Breeding has been recorded throughout the year (Riveros-Salcedo and Jahncke Aparicio 1990, Jahncke and Goya 1998), with least activity in November. There are two breeding periods, with some evidence that individual birds breed twice annually (Riveros-Salcedo and Jahncke Aparicio 1990, Jahncke and Goya 1998, M. de L. Brooke verbally 2000). In the non-breeding season, it occurs close to breeding islands in the rich upwelling waters of the Humboldt Current. In Peru, it feeds, even in heavily fished areas, on small crustaceans and small fish (mostly larvae) (Jahncke et al. 1999). At La Vieja Island, Peru, Peruvian anchovy Engraulis ringens (33.9%), the small krill Euphausia mucronata (26.8%) and squat lobster Pleuroncodes monodon (24.3%) were the most important prey species (García-Godos and Goya 2006). High monthly variability in the main prey species suggests an opportunistic feeding behaviour associated with prey avaliability (García-Godos and Goya 2006).

Pelecanoides garnotii formerly bred on offshore islands from Isla Lobos de Tierra, Peru, to Isla Chiloé, Chile. It was numerous, e.g. there were c.100,000 pairs, and perhaps more, on Isla Chañaral, Chile, in 1938 (Vilina 1992), but the population has since declined significantly. Overall, the largest breeding colonies are attributed to the La Vieja-San Gallán islands in Peru and Choros islands in Chile, separated by 1,300 km (C. E. Fernández et al. in litt. 2020). In Peru, there were c.12,000-13,000 pairs on San Gallán and La Vieja Islands in 1995-1996 (Jahncke and Goya 1998). This is considerably higher than the c.1,500 individuals estimated in the early 1990s, probably because of improved information rather than an actual increase. In May-August 2010 a new survey of the La Vieja Islands documented 102,343 active nests (c.95% on La Vieja), of which 36,450 were occupied, indicating at least a three-fold increase in pairs since 1996, and possibly significantly more (C. Zavalaga in litt. 2010). Two small colonies were found on Corcovado Island, Peru in 2005, extending the current breeding distribution c.700 km north of La Vieja, a main breeding centre (Valverde 2006). A colony may also be present again on the Lobos de Afuera Islands where two individuals were sighted in 2003 and 2004 (Figueroa and Stucchi 2008). 
Recently, new colonies have been found on Lobos de Afuera and Corcovado suggesting the species's reappearance there (E. Frere in litt. 2020). In Chile, 220 nests were also found on Isla Pan de Azúcar in the late 1980s, where 500+ were seen offshore in November 1993 (S. N. G. Howell in litt. 1999), and 300 nests were reported on Isla Choros in the late 1980s, which had increased to an estimated 1,550 active nests in 2001-2003 (Simeone et al. 2003). However, high densities of nests were recorded on 4 islands north of Chile (Chañaral, Damas, Choros and Gaviota islands), with suggested densities of up to 1,400 individuals per hectare (Cruz-Jofré and Vilina 2014).  

It has been recorded throughout the year near Isla Chañaral, and may still breed there or on small islands to the south (Vilina 1992). A more recent survey found evidence of the species entering artificial burrows on Chañaral, with footprints observed in social attraction sites; however, no nesting has yet been observed (C. Wolf and N. Holmes in litt. 2020). 

Conservation Actions Underway
All colonies are in reserves but only La Vieja has trained guards (Jahncke et al. 1999). The Humboldt Penguin National Reserve additionally includes Isla Choros and the surrounding marine area (Cristofari et al. 2019). Pan de Azúcar is declared a National Park, with a management plan granted in 2002, Choros is also a National Reserve with a management plan granted in 2009, whilst Grande de Atacama is a Coastal Marine Protected Area (Fernández et al. 2019). There have been searches for additional colonies in Chile (Vilina 1992). Strong biosecurity measures are in place on Choros and Chañaral Islands (due to the National Forest Corporation's [CONAF] management of the Humboldt Penguin National Reserve), albeit other breeding sites may be lacking in this (C. Wolf and N. Holmes in litt. 2020). A rabbit eradication programme conducted on Choros Island in 2013 was observed to have led to higher densities of the species post-eradication (C. Wolf and N. Holmes in litt. 2020).  Similar eradication programmes were also carried out on Chañaral Island in 2016 (C. Wolf and N. Holmes in litt. 2020). In December 2009, 22 guano islands, 11 peninsulas (guano reserves) and adjacent waters, covering about 140,000 ha including 3 km offshore, were added to Peru’s national protected area system (Harrison 2009). Island Conservation and Chile's Forest Service (CONAF) are attempting to attract nesting on Chañaral Island by decoys, artificial nests, and play-back (A. Simeone et al. in litt. 2020), albeit breeding has not yet been observed (American Bird Conservancy 2020, Vilches et al. 2020). 

Conservation Actions Proposed
Conduct extensive research on the biology of the species (Carboneras et al. 2020). Implement local conservation work on breeding populations and improve regular monitoring programmes (Cristofari et al. 2019, Fernández et al. 2019, C. Wolf and N. Holmes in litt. 2020). Implement invasive mammal eradication projects on historic and potentially new nesting sites such as Pajaros Uno (Chile) and Chincha Norte (Peru) (C. Wolf and N. Holmes in litt. 2020). Address the complex issue of guano extraction (M. de L. Brooke in litt. 1999). Provide artificial burrows (M. de L. Brooke in litt. 1999). Control predators on breeding islands. Survey islands close to Corcovado Island, Peru with similar characterisitics for breeding sites (Valverde 2006). Establish permanent monitoring of the largest colony at La Vieja Island (García-Godos and Goya 2006).