[abridged] The enhanced degrees of deuterium fractionation observed in envelopes around protostars demonstrate the importance of chemistry at low temperatures, relevant in pre- and protostellar cores. formaldehyde is an important species in the formation of methanol and more complex molecules. Here, we present the first study of formaldehyde deuteration on small scales around the prototypical low-mass protostar IRAS 16293-2422 using high spatial and spectral resolution Atacama Large Millimeter/submillimeter Array (ALMA) observations. Numerous isotopologues of formaldehyde are detected, among them H$_2$C$^{17}$O, and D$_2^{13}$CO for the first time in the ISM. The large range of upper energy levels covered by the HDCO lines help constrain the excitation temperature to 106$\pm$13 K. Using the derived column densities, formaldehyde shows a deuterium fractionation of HDCO/H$_2$CO=6.5$\pm$1%, D$_2$CO/HDCO=12.8$^{+3.3}_{-4.1}$%, and D$_2$CO/H$_2$CO=0.6(4)$\pm$0.1%. The isotopic ratios derived are $^{16}$O/$^{18}$O=805, $^{18}$O/$^{17}$O=3.2 and $^{12}$C/$^{13}$C=56. The HDCO/H$_2$CO ratio is lower than found in previous studies, highlighting the uncertainties involved in interpreting single dish observations of the inner warm regions. The D$_2$CO/HDCO ratio is only slightly larger than the HDCO/H$_2$CO ratio. This is consistent with formaldehyde forming in the ice as soon as CO has frozen onto the grains, with most of the deuteration happening towards the end of the prestellar core phase. A comparison with available time-dependent chemical models indicates that the source is in the early Class 0 stage.Read less <