ABSTRACT Clinical relevance Optical coherence tomography angiography (OCT-A) may enable the identification of alteration in the retinochoroidal microvasculature in patients with iron deficiency anaemia. Background To investigate the presence of macular microvascular alterations in females with IDA by using OCT-A. Methods This is a cross-sectional comparative study. Forty patients with IDA and 35 age-matched healthy women underwent a complete ophthalmologic examination and OCT-A imaging. Foveal avascular zone parameters and the vessel density in the superficial (SCP) and deep capillary plexus (DCP) were calculated using automated software. All measurements were compared between groups. Correlations between the OCT-A metrics and haematological laboratory parameters were evaluated. Results Compared to healthy subjects, IDA patients revealed significantly decreased vessel density of the SCP in all parafoveal quadrants (p < 0.05). In contrast, vessel density analysis in DCP has shown no statistically significant difference in all parafoveal quadrants (p > 0.05). Although foveal vessel density in both SCP and DCP were higher in the IDA group, only the foveal vessel density in DCP was significantly higher than controls (p = 0.001). The mean values of the foveal avascular zone area and perimeter and choriocapillaris flow area were significantly lower in the IDA group (p < 0.05). The parafoveal vessel density in SCP, foveal avascular zone area, and choriocapillaris flow area were positively correlated with haematological parameters including haemoglobin, haematocrit, mean corpuscular haemoglobin, and mean corpuscular volume (p < 0.01). Conclusion Patients with IDA had decreased parafoveal vessel density in the SCP, but not the DCP. Foveal avascular zone metrics and choriocapillaris flow area measurements were significantly lower in IDA.