Context. 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. Aims. Here, we aim to 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. We determine the excitation temperature, abundances and fractionation level of several formaldehyde isotopologues, including its deuterated forms. Methods. Excitation temperature and column densities of formaldehyde in the gas close to one of the components of the binary were constrained through modeling of optically thin lines assuming local thermodynamical equilibrium. The abundance ratios were compared to results from previous single dish observations, astrochemical models and local ISM values. Results. Numerous isotopologues of formaldehyde are detected, among them H₂C¹⁷O, and D₂¹³CO 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 ± 13 K. Using the derived column densities, formaldehyde shows a deuterium fractionation of HDCO/H₂CO = 6.5 ± 1%, D₂CO/HDCO = 12.8_–4.1^+3.3%, and D₂CO/H₂CO = 0.6(4) ± 0.1%. The isotopic ratios derived are ¹⁶O/¹⁸O = 805_–79⁺⁴³, ¹⁸O/¹⁷O = 3.2_–0.3^+0.2, and ¹²C/¹³C = 56_–11⁺⁸. Conclusions. The HDCO/H₂CO ratio is lower than that found in previous studies, highlighting the uncertainties involved in interpreting single dish observations of the inner warm regions. The D₂CO/HDCO ratio is only slightly larger than the HDCO/H₂CO 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 toward 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.