In this paper we discuss a general notion of Weil cohomology theories, both in algebraic geometry and in rigid analytic geometry. We allow our Weil cohomology theories to have coefficients in arbitrary commutative ring spectra. Using the theory of motives, we give three equivalent viewpoints on Weil cohomology theories: as a cohomology theory on smooth varieties, as a motivic spectrum and as a realization functor. We also associate to every Weil cohomology theory a motivic Hopf algebroid generalizing the construction we gave in Ayoub (2014) for the Betti cohomology. Exploiting results and constructions from Ayoub (2020), we are able to prove that the motivic Hopf algebroids of all the classical Weil cohomology theories are connective. In particular, they give rise to motivic Galois groupoids which are spectral affine groupoid schemes.