PURPOSE: To commission a beam model in ClearCalc (Radformation Inc.) for use as a secondary dose calculation algorithm and to implement its use into an adaptive workflow for an MR-linear accelerator. METHODS: A beam model was developed using commissioning data for an Elekta Unity MR-linear accelerator and entered into ClearCalc. The beam model consisted of absolute dose calculation settings, output factors, percent depth-dose (PDD) curves, mutli-leaf collimator (MLC) transmission and dose leaf gap error, and cryostat corrections. Beam profiles were hard-coded by the manufacturer into the beam model and were compared with Monaco-derived profiles. The beam model was tested by comparing point doses in a homogenous phantom obtained through measurements using an ionization chamber in water, Monaco, and ClearCalc for various field sizes, source-surface distances (SSDs), and point locations. Additional testing including point dose verification for test plans using a heterogeneous phantom and patient plans. Post clinical implementation, performance of ClearCalc was evaluated for the first 41 patients treated, which included 215 adaptive plans. RESULTS: PDDs generated using ClearCalc fell within 1.2% of measurements. Field profile comparison between ClearCalc and Monaco showed an average pass rate of 98% using a 3%/3 mm gamma criteria. Measured cryostat corrections used in the beam model showed a maximum deviation from unity of 1.4%. Point dose and field monitor units (MUs) comparisons in a homogenous phantom (N = 22), heterogeneous phantoms (N = 22), and patient plans (N = 57) all passed with a threshold of 5%/5MU. Clinically, ClearCalc was implemented as a physics check post adaptive planning completed prior to beam delivery. Point dose and field MUs showed good agreement at a 5%/5MU threshold for prostate stereotactic body radiation therapy (SBRT), pelvic lymph nodes, rectum, and prostate and lymph node plans. DISCUSSION: This work demonstrated commissioning and clinical implementation of ClearCalc into an adaptive planning workflow. No primary or adaptive plan failures were reported with proper beam model testing.