A comprehensive understanding of membrane protein (MP) folding in the native-like environment is one of the most formidable challenges in protein biophysics. Folding of alpha-helical MPs has been described by a model featuring two energetically and mechanistically distinct stages involving (i) the translocon-mediated insertion and formation of individual helices, and (ii) the assembly of helices into helical bundles. A potential third stage had been proposed which includes interactions such as folding of loops and binding of ligands. It may play a crucial role in the formation of a functional and stable protein; however, the nature of this stage is yet to be elucidated. In our research, we aim to probe interactions contributing to MP stability within the lipid bilayer and to provide evidence for the third folding stage. Here, we developed a methodology that combines hydrogen-deuterium exchange (HDX) and solid-state NMR (ssNMR) detection to site-specifically follow the thermally induced unfolding events of MPs in their lipid environment. We first employed this methodology to obtain an atomistic description of the thermally induced unfolding pathway of a retinal-binding photoreceptor Anabaena Sensory Rhodopsin (ASR). The pathway is visualized through ssNMR-detected snapshots of HDX patterns as a function of temperature, revealing the unfolding iii intermediate and its stabilizing factors involving interactions within the retinal binding pocket and at the intermonomer interface. This methodology was then implemented for investigating the unfolding energy landscape of human aquaporin-1 (hAQP1), a homotetrameric transmembrane water channel. Site-specific exchange rates were probed at four different temperatures and the activation energies were extracted, from which we constructed an unfolding energy landscape. We described the specific unfolding events correlated to the unfolding transitions, and structurally characterized the unfolding intermediates. The heat-induced unfolding follows a two-step process: the first step involves an activation barrier corresponding to the unfolding of an extracellular loop which destabilizes the transmembrane domain and serves as a precursor of cooperative unfolding over an additional activation barrier in the second step. Our results suggest that the folding of this loop plays a critical role in stabilizing the correct fold of the entire protein, which is further supported by site-directed mutagenesis experiments.