The use of decellularized tendon tissue as a scaffold for tendon tissue engineering provides great opportunities for future clinical and current research applications. The aim of this study was to assess the effect of repetitive freeze-thaw cycles and two different detergents, t-octyl-phenoxypolyethoxyethanol (Triton X-100) and sodium dodecyl sulfate (SDS), on decellularization effectiveness and cytocompatibility in large tendons. Freshly collected equine superficial and deep digital flexor tendons were subjected to decellularization according to four different protocols (1 and 2: freeze-thaw cycles combined with either Triton X-100 or SDS; 3 and 4: Triton X-100 or SDS). Decellularization effectiveness was assessed based on the reduction of vital cell counts, histologically visible nuclei, and DNA content. Transmission electron microscopy was performed to evaluate cellular and extracellular matrix integrity. Further, cytocompatibility of scaffolds that had been decellularized according to the protocols including freeze-thaw cycles (protocols 1 and 2) was assessed by seeding the scaffolds with superparamagnetic iron oxide labeled mesenchymal stromal cells and monitoring the cells histologically and by magnetic resonance imaging for two weeks. Decellularization was significantly more effective when using the protocols including freeze-thaw cycles, leaving only roughly 1% residual nuclei and 20% residual DNA, whereas samples that had not undergone additional freeze-thaw cycles contained roughly 20% residual nuclei and 40% residual DNA. No morphological extracellular matrix alterations due to decellularization could be observed. Scaffolds prepared by both protocols including freeze-thaw cycles were cytocompatible, but the cell distribution into the scaffold tended to be better in scaffolds that had been decellularized using freeze-thaw cycles combined with Triton X-100 instead of SDS.