Cell-populated collagen gels have provided significant insight into the cellular contractile mechanisms and cell-matrix interactions that are necessary for compacting and remodeling extant matrix. Nevertheless, little research has been devoted towards determining how cells entrench these deformations that contribute to establishing a preferred mechanical state. To this end, we examined the roles of two covalent matrix cross-linkers, i.e. tissue transglutaminase and lysyl oxidase, during global remodeling of the free-floating fibroblast-populated collagen lattice. Inhibition of tissue transglutaminase resulted in a reduced rate of compaction compared to controls during early remodeling (up to 2 days). In contrast, inhibition of lysyl oxidase did not alter the early compaction of these lattices, but it reduced the compaction after 2 days of culture. Acute inhibition of different contractile mechanisms suggested further that calcium-dependent contractility may have dominated during the initial remodeling of the collagen lattice before giving way to calcium-independent contractility at later times. In summary, these findings suggest that early remodeling of the free-floating collagen lattice is facilitated by calcium-dependent cell contraction while entrenchment is dominated by a tissue transglutaminase-mediated cross-linking of the extant matrix. As remodeling continues, however, lysyl oxidase increases its contribution, perhaps by consolidating de novo collagen fibrils into fibers to continue the remodeling while the cells transition to a more sustained, calcium-independent contractility. These results promise to influence future tissue engineering studies as well as computational simulations aimed at understanding matrix remodeling in complex in vivo situations.