Learning the topology of higher-order networks from data is a fundamental challenge in many signal processing and machine learning applications. Simplicial complexes provide a principled framework for modeling multi-way interactions, yet learning their structure is challenging due to the strong coupling across different simplicial levels imposed by the inclusion property. In this work, we propose a joint framework for simplicial complex learning that enforces the inclusion property through a linear constraint, enabling the formulation of the problem as a binary linear program. The objective function consists of a combination of smoothness measures across all considered simplicial levels, allowing for the incorporation of arbitrary smoothness criteria. This formulation enables the simultaneous estimation of edges and higher-order simplices within a single optimization problem. Experiments on simulated and real-world data demonstrate that the proposed joint approach outperforms hierarchical and greedy baselines, while more faithfully enforcing higher-order structural priors.