Three new fluorinated mixed valence Fe(II)–Fe(III) phosphites were synthesized by employing mild hydrothermal conditions. (H4baepn)0.5[FeIII2.3FeII1.7(H2O)2(HPO3)4−(x+y)(HPO4)x(PO4)yF4] (x [similar, equals] 0.13, y [similar, equals] 0.3) (1) (baepn = N,N′-bis(2-aminoethyl)-1,3-propanediamine (C7N4H20)) and the Co(II)-substituted phase with the formula (H4baepn)0.5[FeIII2.0FeII0.71CoII1.29(H2O)2(HPO3)4−x(HPO4)xF4] (x [similar, equals] 0.38) (2) were studied by single crystal X-ray diffraction. The phase with the major content of Co(II), (H4baepn)0.5[FeIII2.0FeII0.62CoII1.38(H2O)2(HPO3)4−x(HPO4)xF4] (x [similar, equals] 0.38) (3) was obtained as a polycrystalline powder and studied by Rietveld refinement by using the structural model of 2. These compounds were characterized by ICP-Q-MS, thermogravimetric and thermodiffractometric analyses, and XPS, IR, UV/vis and Mössbauer spectroscopy. The single crystal data indicate that phases 1 and 2 crystallize in the P21/c space group with lattice parameters a = 13.6808(4), b = 12.6340(2), c = 12.7830(3) Å and β = 116.983(4)° for 1 and a = 13.6823(4), b = 12.6063(3), c = 12.7535(4) Å and β = 116.988(4)° for 2, with Z = 4. The reciprocal space of 1 shows satellite reflections with a modulation wavevector q = 0.284(2)a* which indicate an incommensurate long-range order. The average structure of these compounds is built up by a 3D lattice constructed by inorganic layers of Fe(III) chains and Fe(II) and Co(II) dimers joined by phosphite groups partially substituted by HPO4 and PO4 tetrahedral groups. These anionic layers stack along the [100] direction encapsulating linear tetramines in eight-membered open channels involving host–guest interactions. Magnetic measurements of 1 and 3 showed antiferromagnetic coupling as the major interactions, exhibiting a weak ferromagnetic component together with a spin glass transition at low temperature in the case of 1. Heat capacity measurements showed a small anomaly at 20.5 K for 1 and a sharp magnetic peak at 28 K for 3. Unexpectedly, the small anomaly observed in 1 increased with the magnetic field and became better defined.