While the standard formulation of quantum theory assumes a fixed background causal structure, one can relax this assumption within the so-called process matrix framework. Remarkably, some processes, termed causally nonseparable, are incompatible with a definite causal order. We explore a form of certification of causal nonseparability in a semi-device-independent scenario where the involved parties receive trusted quantum inputs, but whose operations are otherwise uncharacterized. Defining the notion of causally nonseparable distributed measurements, we show that certain causally nonseparable processes that cannot violate any causal inequality, including the canonical example of the quantum switch, can generate noncausal correlations in such a scenario. Moreover, by imposing some further natural structure to the untrusted operations, we show that all bipartite causally nonseparable process matrices can be certified with trusted quantum inputs.