Background: To assess the ability of low-dose dual-energy computed tomography (ld-DECT) virtual non-calcium (VNCa) images for detecting bone marrow pathologies of the sacroiliac joints (SIJs) in patients with axial spondyloarthritis (axSpA). Material and Methods: Sixty-eight patients with suspected or proven axSpA underwent ld-DECT and MRI of the SIJ. VNCa images were reconstructed from DECT data and scored for the presence of osteitis and fatty bone marrow deposition by two readers with different experience (beginner and expert). Diagnostic accuracy and correlation (Kohen’s k) with magnetic resonance imaging (MRI) as the reference standard were calculated for the overall and for each reader separately. Furthermore, quantitative analysis was performed using region-of-interest (ROI) analysis. Results: Twenty-eight patients were classified as positive for osteitis, 31 for fatty bone marrow deposition. DECT’s sensitivity (SE) and specificity (SP) were 73.3% and 44.4% for osteitis and 75% and 67.3% for fatty bone lesions, respectively. The expert reader achieved higher diagnostic accuracy for both osteitis (SE 93.33%; SP: 51.85%) and fatty bone marrow deposition (SE: 65%; SP: 77.55%) than the beginner (SE: 26.67%; SP: 70.37% for osteitis; SE: 60%; SP: 44.9% for fatty bone marrow deposition). Overall correlation with MRI was moderate (r = 0.25, p = 0.04) for osteitis and fatty bone marrow deposition (r = 0.25, p = 0.04). Fatty bone marrow attenuation in VNCa images (mean: −129.58 HU; ±103.61 HU) differed from normal bone marrow (mean: 118.84 HU, ±99.91 HU; p < 0.01) and from osteitis (mean: 172 HU, ±81.02 HU; p < 0.01) while osteitis did not differ significantly from normal bone marrow (p = 0.27). Conclusion: In our study, low-dose DECT failed to detect osteitis or fatty lesions in patients with suspected axSpA. Thus, we conclude that higher radiation might be needed for DECT−based bone marrow analysis.