This work discusses scalar–tensor theories of gravity, with a focus on the Brans–Dicke sub-class, and one that also takes note of the latter’s equivalence with f(R) gravitation theories. A 1+3 covariant formalism is used in this case to discuss covariant perturbations on a background Friedmann–Laimaître–Robertson–Walker (FLRW) spacetime. Linear perturbation equations are developed based on gauge-invariant gradient variables. Both scalar and harmonic decompositions are applied to obtain second-order equations. These equations can then be used for further analysis of the behavior of the perturbation quantities in such a scalar–tensor theory of gravitation. Energy density perturbations are studied for two systems, namely for a scalar fluid-radiation system and for a scalar fluid-dust system, for Rn models. For the matter-dominated era, it is shown that the dust energy density perturbations grow exponentially, a result which agrees with those already existing in the literatures. In the radiation-dominated era, it is found that the behavior of the radiation energy–density perturbations is oscillatory, with growing amplitudes for n>1, and with decaying amplitudes for 0<n<1. This is a new result.