M. hyopneumoniae is an economically significant swine pathogen with a predilection for attaching to ciliated epithelial cells lining the trachea, bronchi and bronchioles in the upper respiratory tract. Colonisation of epithelial cilia causes ciliostasis and epithelial cell death, effectively compromising the mucociliary escalator. These events predispose swine lungs to secondary bacterial and viral pathogens further exacerbating losses through increased morbidity and mortality. Members of the P97 and P102 paralog families are important cilium adhesins. Our studies have shown that these molecules are targets of multiple endoproteolytic processing events that generate a large number of cleavage fragments on the surface of M. hyopneumoniae. It order to understand the biological significance of endoproteolysis we used a series of systems-wide affinity chromatography protocols to identify binding sites for range of host molecules including fibronectin, plasminogen, heparin and actin. The affinity protocols recovered the dominant cleavage fragments and a series of low abundance cleavage fragments highlighting the complex nature of the endoproteolytic events that shape the surface protein topography of this pathogen. Using Mhp183 as a representative of the P97 adhesin family, we show how the C-terminus of P97 contains a multifunctional binding domain. Overlapping peptides were used to map essential binding sites and the binding interactions were independently confirmed using quantitative binding assays.