Health in pregnancy and infancy can affect the risk of chronic non-communicable diseases. We aimed to describe leptin and adiponectin concentrations in low birth weight (LBW) infants and identify possible associations with maternal nutritional status, adequacy for gestational age, nutritional recovery, and current dietary intake. A cross-sectional study with LBW infants (9–12 months) including maternal background and pre-pregnancy nutritional condition was performed. From the Infants: anthropometry at birth and current was expressed as z-score (weight: WAZ, length, head circumference), nutritional recovery, dietary intake, leptin, and adiponectin blood concentrations. The mean age of the 54 infants was 10.0 ± 1.5 months, 32 (59.3%) were female, 36 (66.7%) preterm, 23 (42.6%) small for gestational age (SGA), and 25 pregnancies (46.3%) were twin. Almost all (98%) of the infants intake energy and protein above the recommendation, and 47 (87.6%) consumed ultra-processed foods. At the time of the assessment, 8 (14.8%) were overweight and 4 (7.4%) had short stature. SGA infants showed faster weight recovery (WAZ 1.54; 95% CI 1.17, 1.91; p = 0.001), higher leptin’s concentration (3.0 ng/ml (1.7, 3.0) versus 1.6 ng/ml (0.9, 2.6); p = 0.032)), and leptin/adiponectin ratio (0.13 ± 0.08 versus 0.07 ± 0.07; p = 0.018). The pre-gestational BMI was a modifier of the effect of WAZ on leptin levels (p = 0.027) in LBW infants. Higher pre-gestational BMI increased the effect of WAZ variation (birth and current) on leptin levels. Concluding, LBW infants showed early changes in leptin and adiponectin concentrations, influenced by maternal (pre-gestational BMI), intrauterine (gestational age adequacy – SGA), and postnatal weight gain. This combination of factors may increase the risk of NCD for this group of children.