We study how matter-wave interferometry with Bose-Einstein condensates is affected by hypothetical collapse models and by environmental decoherence processes. Motivated by recent atom fountain experiments with macroscopic arm separations, we focus on the observable signatures of first-order and higher-order coherence for different two-mode superposition states, and on their scaling with particle number. This can be used not only to assess the impact of environmental decoherence on many-body coherence, but also to quantify the extent to which macrorealistic collapse models are ruled out by such experiments. We find that interference fringes of phase-coherently split condensates are most strongly affected by decoherence, whereas the quantum signatures of independent interfering condensates are more immune against macrorealistic collapse. A many-body enhanced decoherence effect beyond the level of a single atom can be probed if higher-order correlations are resolved in the interferogram.