The structure of HPM-3, a layered aluminophosphate prepared using 1,2,3-trimethylimidazolium (123TMI) as an organic structure-directing agent by the fluoride route, has been solved by continuous rotation electron diffraction (cRED), and Rietveld refined against synchrotron powder X-ray diffraction data. Charge balance of the occluded cation is achieved through F- anions and dangling Al(OP)3OH groups. Half of the Al is pentacoordinated in negatively charged Al(OP)4-F-Al(OP)4 pairs. The layers in HPM-3, denoted as jsn, are observed in the fully connected metalloaluminophosphate molecular sieves with JSN topology. Thus, HPM-3 can be a precursor to a JSN metal-free aluminophosphate if a topotactic condensation can be reached, which proved to be difficult but feasible. Treatments under different conditions resulted in a number of known (PST-27 and AlPO4-5 by a disruptive transformation) or new phases (through mild thermal treatments). Among the latter, a layered phase with a shorter interlayer space, denoted as HPM-3S, contains half the amount of organic as HPM-3. This is afforded by the capability of 123TMI compounds to sublimate at relatively low temperatures. HPM-3S still contains the same jsn layers. Therefore, the transformation of HPM-3 into HPM-3S is topotactic but without reaching condensation. Among the phases appearing under calcination conditions at relatively low temperature (<350 °C), we observed solids compatible with the JSN topology, but with poor crystallinity. This is attributed to a wrong alignment in HPM-3 of the dangling Al(OP)3OH and P(OAl)3═O that should connect adjacent layers in a topotactic condensation, which favors 1-dimensional stacking disorder by random shifts of layers during the thermal treatments. However, detemplation at a much lower temperature (175 °C) using O3 finally afforded an aluminophosphate molecular sieve with JSN topology with only moderate stacking disorder. This is just the third reported 2D-to-3D topotactic condensations in aluminophosphates.