Porous magnesium implants are of particular interest for application as resorbable bone substitutes, due to their mechanical strength and a Young’s modulus similar to bone. The objective of the present study was to compare the biocompatibility, bone and tissue ingrowth, and the degradation behaviour of scaffolds made from the magnesium alloys LAE442 (n = 40) and Mg-La2 (n = 40) in vivo. For this purpose, cylindrical magnesium scaffolds (diameter 4 mm, length 5 mm) with defined, interconnecting pores were produced by investment casting and coated with MgF2. The scaffolds were inserted into the cancellous part of the greater trochanter ossis femoris of rabbits. After implantation periods of 6, 12, 24 and 36 weeks, the bone-scaffold compounds were evaluated using ex vivo µCT80 images, histological examinations and energy dispersive x-ray spectroscopy analysis. The La2 scaffolds showed inhomogeneous and rapid degradation, with inferior osseointegration as compared to LAE442. For the early observation times, no bone and tissue could be observed in the pores of La2. Furthermore, the excessive amount of foreign body cells and fibrous capsule formation indicates insufficient biocompatibility of the La2 scaffolds. In contrast, the LAE442 scaffolds showed slow degradation and better osseointegration. Good vascularization, a moderate cellular response, bone and osteoid-like bone matrix at all implantation periods were observed in the pores of LAE442. In summary, porous LAE442 showed promise as a degradable scaffold for bone defect repair, based on its degradation behaviour and biocompatibility. However, further studies are needed to show it would have the necessary mechanical properties required over time for weight-bearing bone defects.