Background Iron Deficiency Anaemia (IDA) is reportedly high in pregnant adults and the causes well studied. However, among pregnant teenagers, the levels and associated factors of IDA are not fully understood. Methods In a prospective cohort study among Ghanaian pregnant teenagers, aged 13–19 years, IDA prevalence and associated factors were investigated. Sociodemographic data, household hunger scale (HHS), lived poverty index (LPI), FAO’s women’s dietary diversity score (WDDS) and interventions received during antenatal care (ANC) were obtained from 416 pregnant teenagers in Ashanti Region, Ghana. Micronutrient intakes using a repeated 24-hour dietary recall, and mid-upper arm circumference (MUAC) were determined and blood samples analysed for haemoglobin (Hb), serum levels of ferritin, prealbumin, vitamin A, total antioxidant capacity (TAC), C-reactive protein (CRP), and zinc protoporphyrin (ZPP). Results Anaemia (Hb cutoff <11.0 g/dL) was 57.1%; deficient systemic supply of iron stores (31.4%), depleted body stores of iron (4.4%), inadequate dietary iron intake (94.5%), and inadequate multiple micronutrient intakes (49.5%), were all notable among study participants. Between-subject effects using Generalized Linear Modelling indicated malaria tablet given at ANC (p = 0.035), MUAC (p = 0.043), ZPP (p<0.001), ZPP/Hb ratio (p<0.001) and depleted body iron stores (DBIS) (p<0.001) to significantly affect Hb levels. Pregnant teenagers with a high ZPP/Hb ratio (OR = 9.7, p<0.001, 95%CI = 6.0–15.8) had increased odds of being anaemic compared to those with normal ZPP/Hb ratio. Participants who were wasted (OR = 1.2, p = 0.543, 95%CI = 0.6–2.3), and those with depleted iron stores (OR = 3.0, p = 0.167, 95%CI = 0.6–14.6) had increased odds of being anaemic. Participants who experienced hunger were close to 3 times more likely (OR = 2.9, p = 0.040, 95%CI = 1.1–7.8) for depleted iron stores, compared to those who did not experience hunger. Also, participants with inadequate multiple micronutrients intakes (OR = 2.6, p = 0.102, 95%CI = 0.8–8.4), and those with low serum levels of ferritin (OR = 3.3, p = 0.291, 95%CI = 0.4–29.2) had increased odds of depleted body iron stores. Conclusions IDA is common among pregnant teenagers and the related factors include malaria tablets given at ANC, maternal hunger, maternal MUAC, a deficient systemic supply of iron, depleted body iron stores, ZPP, and ZPP/Hb ratio. Appropriate interventions are urgently needed to address the causes of IDA among pregnant teenagers.