Low-dose electron diffraction has been instrumental in determining the crystal structures of two compounds with metal-radical coordination frameworks {[MnII2(NITIm)3]CF3SO3.CH3OH}n (1) and {[MnII2(NITImMe2)3]ClO4}n (2) that could never be grown to a crystal size large enough for single-crystal X-ray diffraction characterization. The compounds crystallize as nanocrystals upon addition of triflate (1) and perchlorate (2) anions and coordination of manganese(II) with bis-chelate nitronyl nitroxide radicals NITImH (1) and NITImHMe2 (2) which are respectively 2-(2-imidazolyl)- and 2-(4,5-dimethylimidazol-2-yl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazol-3-oxide-1-oxyl. The two compounds have layered crystal structures in which cationic 2D metal-radical coordination polymers {[MnII2(NITIm)3]+}n (1) and {[MnII2(NITImMe2)3]+}n (2) are separated by layers of triflate (1) or perchlorate (2) anions. Magnetic measurements evidence a ferrimagnetic behavior within the 2D metal-radical sheets due to alternating antiferromagnetically coupled spins (SMn2+ = 5/2 and Sradical = 1/2). Both compounds exhibit a long-range 3D ordering of weak-ferromagnetic type due to spin canting with Curie temperatures Tc = 45 K (1) and 40 K (2). This is associated with a field-induced metamagnetic transition from antiferromagnetic to ferromagnetic coupling of 2D metal-radical sheets. Studies of the crystal structures allows to rationalize how the molecular structure of nitronyl nitroxide radicals and of the counter-anions along with crystal packing affect the magnetic behavior related to interlayer distance and framework flexibility. These results are striking evidence that electron crystallography is a unique tool to solve structures of metal-organic compounds crystallizing as nanocrystals even with nitronyl nitroxide radical components too sensitive to typical electron doses. Overcoming the crystal size barrier, it allows the validation of chemical synthesis and the establishment of magneto-structural relationships fostering new advances in the design of molecule-based magnets.