Portable X-ray fluorescence is a new tool in the study of human bone. This research aims to investigate if variations in bone elemental concentrations are related with porous skeletal lesions (PSLs). One hundred well-preserved non-adult skeletons aged 0–11 years were selected from the archaeological site Convent of São Domingos, Lisbon (18th–19th century). Measuring a standard reference material and calculating the technical error of measurement assured elemental data reliability. Moreover, measuring soil samples excluded possible contamination of bones with elements from the soil, except for Pb. Additionally, the Ca/P ratio indicates maintenance of bone integrity. Cribra cranii, orbitalia, humeralis, and femoralis were recorded as present/absent, and the estimated intra-/inter-observer errors were low. The multivariate analysis found higher odds of having cribra orbitalia (OR = 1.76; CI = 0.97–3.20) and cribra femoralis (OR = 1.42; CI = 0.73–2.74) in individuals with lower Fe and higher S. Furthermore, higher levels of P, Ca, and Sr increased the odds of individuals developing cribra femoralis (OR = 2.30; CI = 1.23–4.29). Age also correlated with increased odds of exhibiting cribra orbitalia (OR = 1.86; CI = 0.94–3.68), cribra femoralis (OR = 6.97; CI = 2.78–17.45), and cribra humeralis (OR = 8.32; CI = 2.71–25.60). These findings suggest a shared etiology for these three cribras, contrasting with the higher Fe levels in individuals with cribra cranii. Lower Fe and higher S levels in individuals with cribra suggest a complex etiology, possibly involving conditions like megaloblastic or chronic disease anemia(s). Age-related elemental changes support the hypothesis that age influences cribra frequencies. This study highlights PSL complexity and opens new avenues for research.