We derive electronic tight-binding Hamiltonians for strained graphene, hexagonal boron nitride, and transition-metal dichalcogenides based on Wannier transformation of ab initio density functional theory calculations. Our microscopic models include strain effects to leading order that respect the hexagonal crystal symmetry and local crystal configuration and are beyond the central force approximation which assumes only pairwise distance dependence. Based on these models, we also derive and analyze the effective low-energy Hamiltonians. Our ab initio approaches complement the symmetry group representation construction for such effective low-energy Hamiltonians and provide the values of the coefficients for each symmetry-allowed term. These models are relevant for the design of electronic device applications since they provide the framework for describing the coupling of electrons to other degrees of freedom including phonons, spin, and the electromagnetic field. The models can also serve as the basis for exploring the physics of many-body systems of interesting quantum phases.