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Disentangling the role of competition in regulating the distribution of sympatric species can be difficult because species can have different habitat preferences or time use that introduce non-random patterns that are not related to interspecific interactions. We adopted a multi-step approach to systematically incorporate habitat preferences while investigating the co-occurrence of two presumed competitors, morphologically similar, and closely related ground-dwelling birds: the brown tinamou (Crypturellus obsoletus) and the tataupa tinamou (C. tataupa). First, we used single-species occupancy models to identify the main landscape characteristics affecting site occupancy, while accounting for detection probability. We then used these factors to control for the effect of habitat while investigating species co-occurrence. In addition, we investigated species present-time partitioning by measuring the degree of overlap in their activity time. Both species were strictly diurnal and their activity time highly overlapped (i.e., the species are not present-time partitioning). The distribution of the two species varied across the landscape, and they seemed to occupy opposite portions of the study area, but co-occurrence models and species interaction factors suggested that the tinamous have independent occupancy and detection. In addition, co-occurrence models that accounted for habitat performed better than models without habitat covariates. The observed co-occurrence pattern is more likely related to habitat preferences, wherein species segregated by elevation. These results provide evidence that habitat characteristics can play a bigger role than interspecific interactions in regulating co-existence of some species. Therefore, exploring habitat preferences while analyzing co-occurrence patterns is essential, in addition to being a feasible approach to achieve more accurate estimation of parameters reflecting species interactions. Occupancy models can be a valuable tool in such modeling.