Summary Background Misbalances in extracellular matrix turnover are key factors in the development of stricturing (Montreal B2) and penetrating (Montreal B3) Crohn's disease. Aim To determine whether serological markers for collagen formation and degradation could serve as biomarkers for complications of Crohn's disease. Methods Serum biomarkers for type I, III, V and VI collagen formation (P1NP, Pro‐C3, Pro‐C5, Pro‐C6) and matrix metalloproteinase mediated degradation (C1M, C3M, C5M and C6M) were measured in a retrospective, single centre cohort of 112 patients with Crohn's disease in the terminal ileum (nonstricturing/nonpenetrating: n=40, stricturing: n=55, penetrating: n=17) and 24 healthy controls. Active inflammation was defined as CRP >5 mg/L. Results C3M and Pro‐C5 levels were higher in penetrating vs nonpenetrating/nonstricturing and stricturing disease (33.6±5 vs 25.8±2.2 P=.004 and 27.2±2.3 P=.018 nmol/L C3M, 1262.7±259.4 vs 902.9±109.9 P=.005 and 953.0±106.4 P=.015 nmol/L Pro‐C5). C1M (71.2±26.1 vs 46.2±6.2 nmol/L P<.001), C3M (31.6±3.9 vs 26.1±1.6 nmol/L P=.002 and Pro‐C5 levels (1171.7±171.5 vs 909.6±80.4 nmol/L P=.002) were higher in patients with active inflammation vs without active inflammation. Pro‐C3/C3M‐ratios were best to differentiate between penetrating vs nonstricturing/nonpenetrating and stricturing disease with area under the curves of 0.815±0.109 (P<.001) and 0.746±0.114 (P=.002) respectively. Conclusions Serological biomarkers show that penetrating Crohn's disease is characterised by increased matrix metalloproteinase‐9 degraded type III collagen and formation of type V collagen. Active inflammation in Crohn's disease is characterised by increased formation of type V collagen and increased matrix metalloproteinase mediated breakdown of type I, III collagen. Pro‐C3/C3M ratios are superior in differentiating between penetrating Crohn's disease vs inflammatory and stricturing Crohn's disease.