We study fourth-order geometric flows on compact Riemannian manifolds, which naturally appear as gradient flows of quadratic curvature functionals. When the Yamabe constant remains bounded from below by a positive constant along the flow, we show that the manifold doesn't collapse, and that a sequence of dilated metrics near a singular time converges to a singularity model. In particular, in dimension four, this assumption is satisfied by a class of gradient flows, provided that the initial energy is less than an explicit constant. The singularities of these flows are then modeled by complete non-compact manifolds, which are Bach-flat and scalar-flat. By combining a Weitzenböck formula with the Sobolev inequality induced by the positivity of the Yamabe constant, we prove several rigidity results for metrics with integral pinched curvature. In particular, we prove a rigidity result for Bach-flat and scalar-flat manifolds in dimension four, which implies that the singularities of our gradient flows can only exist when the initial energy is bigger than a given constant. When this is not the case, these flows exist for all time, and converge to a metric with constant positive curvature. It provides a proof of a "sphere theorem" for closed four-dimensional manifolds with integral pinched curvature. Applying the same method to harmonic forms on an integral pinched manifold, we prove an integral version of the Bochner-Weitzenböck theorem. As a corollary, we obtain the vanishing of Betti numbers under various integral pinching conditions, and we characterize the equality cases.