Energy, in the context of the universe and the models used in describing it , is in the stress energy tensor, which contains the energy/mass transformations.
The accepted at the moment model for the universe is the Big Bang model, as summarized in this plot , is a good fit to the available observations using all known physics to date.
Known physics is encapsulated in the standard model of particle physics. Energy conservation is a strict law within this. In contrast, General Relativity has a grey region on energy conservation.. See also this discussion. As all the data we have from the beginning of the universe are contained in the cosmic microwave background radiation, CMB, in the accepted model for the universe, one can be sure of the modeling from 10^-32 seconds to 380.000 years when the photons decoupled from the soup. There standard model particle physics is used where energy conservation is strict.
The time from the beginning of the universe to the 10^-32 seconds , the end of the inflation period in this plot, the model is completely mathematical as no inflatons have been observed experimentally. Its acceptance is due to its success in describing the homogeneity observed in the CMB.
In any case there is the question "where did the energy come from, to create the Big Bang". This is still a research question with various models proposed.
From 10^-32 seconds and on to the right of the plot, the standard model physics is assumed as holding and there of course energy conservation holds strictly.
The summary is that after 10^-32 seconds the energy residing in the universe is conserved.