The nesting ecology of the Allen Cays rock iguana was studied on Leaf Cay and Southwest Allen's Cay (= U Cay) in the northern Exuma Islands, Bahamas, during 2001 and 2002. Mating occured in mid-May, and females migrated 30–173 m to potential nest sites in mid to late June. Females often abandoned initial attempts at digging nest burrows, and average time from initiation of the final burrow to completion of a covered nest was six days. At least some females completely buried themselves within the burrow during the final stages of burrow construction and oviposition. Females defended the burrow site during the entire time of construction, and most continued that defense for at least three to four weeks after nest completion. Nests were completed between mid-June and mid-July, but for unknown reasons timing was seven days earlier on U Cay than on Leaf Cay. Nest burrows averaged 149 cm in length and terminal nest chambers usually angled off the main burrow. Depth to the bottom of the egg chamber averaged 28 cm, and was inversely correlated with shadiness of the site, suggesting that females may select depths with preferred temperatures (mean, 31.4 C in this study). Overall, only about one in three females nested each year, although nesting frequency increased with female size such that the largest females usually nest annually. Nest fidelity was common, despite the potential for observer effects; seven of 13 two-year nesters placed nests within 0.7 m of that constructed the previous year.

Nesting females averaged 32 cm snout–vent length (SVL) and 1336 g body mass, and larger, older females nested earlier than smaller, younger ones. Sexual maturity is reached at 26–27 cm SVL, about 750 g body mass, and twelve years of age (nearly twice as old as any previously studied lizard). Longevity of females apparently exceeds 40 years. Clutch size ranged from 1–10 eggs (mean 4.6) and was correlated with female body size and age. Eggs averaged 66 mm in length, 35 mm in width, and 49 g in mass. Egg mass was not correlated with female body size, although egg length was negatively correlated, and egg width was positively correlated with female size. The production of elongate eggs in the smaller females allowed them to invest the same total mass in each egg as a larger female, while being constrained by the limits of the pelvic opening. No trade-off existed between standardized clutch size versus egg size. Relative clutch mass (clutch mass/gravid female body mass × 100) averaged 16.5 and did not vary with female size or age. Hatching apparently occurs in late September and early October after about 80–85 days incubation, with emergence within just a few days. Hatchlings averaged 9.5 cm SVL and 33 g body mass. Survivorship to emergence was 78.9%, and was inversely correlated with soil moisture.

The reproductive ecology of other iguanids (sensu strictu) is reviewed for comparison with that of the Allen Cays rock iguana. Comparisons of these data with those available for other rock iguanas of the genus Cyclura suggest that colonization of smaller islands has produced reductions in adult female body size, clutch size, clutch mass, and relative clutch mass, but no change in egg or hatchling mass. Because this pattern is also demonstrated by a population of Cuban iguanas introduced to a small island only 40 years ago, it may primarily be a proximal response to decreased resource availability and/or physiological processability on small islands rather than an evolved response to reduced predation rates or other factors affecting survivorship.