Abstract Aims Women with evidence of ischaemia but no obstructive coronary artery disease (INOCA) often have coronary microvascular dysfunction (CMD). Although invasively measured coronary flow reserve (CFR) is useful for the diagnosis of CMD, intermediate CFR values are often found of uncertain significance. We investigated myocardial flow reserve and left ventricular (LV) structural and functional remodelling in women with suspected INOCA and intermediate CFR. Methods and results Women’s Ischemia Syndrome Evaluation-Coronary Vascular Dysfunction (WISE-CVD) study participants who had invasively measured intermediate CFR of 2.0≤ CFR ≤3.0 (n = 125) were included for this analysis. LV strain, peak filling rate (PFR) and myocardial perfusion reserve index (MPRI) were obtained by cardiac magnetic resonance imaging. Participants were divided: (i) Group 1 (n = 66) high MPRI ≥ 1.8, and (ii) Group 2 (n = 59) low MPRI < 1.8. The mean age was 54 ± 12 years and CFR was 2.46 ± 0.27. MPRI was significantly different but CFR did not differ between groups. LV relative wall thickness (RWT) trended higher in Group 2 and circumferential peak systolic strain and early diastolic strain rate were lower (P = 0.039 and P = 0.035, respectively), despite a similar LV ejection fraction and LV mass. PFR was higher in Group 1 and LV RWT was negatively related to PFR (r = −0.296, P = 0.001). Conclusions In women with suspected INOCA and intermediate CFR, those with lower MPRI had a trend towards more adverse remodelling and impaired diastolic LV function compared with those with higher MPRI. CFR was similar between the two groups. These findings provide evidence that both coronary microvessel vasomotion and structural and functional myocardial remodelling contribute to CMD.