This question does not necessarily have an unambiguous answer, because of the way Ian McDiarmid's makeup varies from scene to scene.
However, some aspects of the question can be dealt with straightforwardly. In some clips, such as this one,
we get a reasonably clear view of Darth Sidious's skin, at least on part of his lower face. There are no prosthetics; the texture of the actor's skin is clearly unmodified.
On the other hand, the skin tone appears different than in the well-lit scenes in which McDiarmid appears as Senator/Chancellor Palpatine. At some level, this is undoubtedly intentional, but it is not always possible to distinguish (even in theory) differences in makeup from differences in lighting. Especially in The Phantom Menace, Sidious's scenes tend to be either in very low light, or his image is being transmitted (in translucent blue) via a video communications link. These effects serve to give him a more sinister appearance, but filming with these different lighting patterns also means using a different makeup on the actor's face.
Screen actors essentially always wear heavy makeup; it's just standard procedure for filming. Moreover, the thickness and the coloration of the makeup will often depend on how a scene is going to be lit. So when McDiarmid was being filmed as Darth Sidious, in poor lighting and with his face mostly hooded, different makeup was required to generate match the effect of the lighting (and both the real studio lighting and the in-universe lighting whose effects are supposed to be shown are relevant). So there is no unambiguous answer to the question: Was the makeup for Darth Sidious different because the character appeared in different light, or because he was supposed to look different?