Abstract We report lensing magnifications, extinction, and time-delay estimates for the first resolved, multiply-imaged Type Ia supernova iPTF16geu, at z = 0.409, using Hubble Space Telescope (HST) observations in combination with supporting ground-based data. Multi-band photometry of the resolved images provides unique information about the differential dimming due to dust in the lensing galaxy. Using HST and Keck AO reference images taken after the SN faded, we obtain a total lensing magnification for iPTF16geu of $μ = 67.8^{+2.6}_{-2.9}$, accounting for extinction in the host and lensing galaxy. As expected from the symmetry of the system, we measure very short time-delays for the three fainter images with respect to the brightest one: -0.23 ± 0.99, -1.43 ± 0.74 and 1.36 ± 1.07 days. Interestingly, we find large differences between the magnifications of the four supernova images, even after accounting for uncertainties in the extinction corrections: $Δ m_1 = -3.88^{+0.07}_{-0.06}$, $Δ m_2 = -2.99^{+0.09}_{-0.08}$, $Δ m_3 = -2.19^{+0.14}_{-0.15}$ and $Δ m_4 = -2.40^{+0.14}_{-0.12}$ mag, discrepant with model predictions suggesting similar image brightnesses. A possible explanation for the large differences is gravitational lensing by substructures, micro- or millilensing, in addition to the large scale lens causing the image separations. We find that the inferred magnification is insensitive to the assumptions about the dust properties in the host and lens galaxy.