Evaluating the entropy production (EP) along a stochastic trajectory requires the knowledge of the system probability distribution, an ensemble quantity notoriously difficult to measure. In this paper we show that the EP of nonautonomous systems in contact with multiple reservoirs can be expressed solely in terms of physical quantities measurable at the single-trajectory level with a suitable preparation of the initial condition. As a result, we identify universal energy and particle fluctuation relations valid for any measurement time. We apply our findings to an electronic junction model, which may be used to verify our prediction experimentally.