We investigate the limit behaviour of sequences of free boundary minimal hypersurfaces with bounded index and volume, by presenting a detailed blow-up analysis near the points where curvature concentration occurs. Thereby, we derive a general quantization identity for the total curvature functional, valid in ambient dimension less than eight and applicable to possibly improper limit hypersurfaces. In dimension three, this identity can be combined with the Gauss-Bonnet theorem to provide a constraint relating the topology of the free boundary minimal surfaces in a converging sequence, of their limit, and of the bubbles or half-bubbles that occur as blow-up models. We present various geometric applications of these tools, including a description of the behaviour of index one free boundary minimal surfaces inside a 3-manifold of non-negative scalar curvature and strictly mean convex boundary. In particular, in the case of compact, simply connected, strictly mean convex domains in R 3 unconditional convergence occurs for all topological types except the disk and the annulus, and in those cases the possible degenerations are classified.Mathematics Subject Classification (MSC 2010): Primary 53A10; Secondary 53C42, 49Q05.which holds true, with the setup as in Theorem 1, for all k sufficiently large. Actually, the second summand on the right-hand side can also be expressed only in terms of topological data (see Subsection 2.3 for a detailed discussion), so that we can derive the formula we will employ in all of our applications:Corollary 7. In the setting of Theorem 1, specified to n = 2, we have for all k sufficiently largewhere χ(Σ j ) denotes the Euler characteristic of Σ j and b j denotes the number of its ends. This is the starting point for our primary geometric applications. We present three instances, which are meant to illustrate the method, and leave other possible extensions in the form of remarks.Here is the first application we wish to discuss: since we can fully classify bubbles and half-bubbles of Morse index less than two (see Corollary 22 and Corollary 24) we can then get novel, unconditional, geometric convergence results for sequences of free boundary minimal