Background: The impact of thermal treatment on acrylamide (ACR) and hydroxymethylfurfural (HMF) formation was investigated for thermally treated sea buckthorn purée. Methods: An optimized procedure for minimizing ACR and HMF formation in thermally treated sea buckthorn purée was described. The precursors of ACR and HMF and their impact in heating of sea buckthorn purée to obtain jam-like products were also evaluated. Results: The contaminant content formed in samples was analyzed on thirteen running variants using a temperature range of 59.3–200.7 °C, and for heating durations between 5.9 and 34.1 min. The calculated equations of contaminant formation in sea buckthorn purée have established that the minimum content is formed at the lowest exposure time, between 10 and 20 min, for both ACR and HMF. The lowest ACR content was attained at 5.9-min exposure time and 130 °C temperature (0.3 µg/kg). For HMF the results revealed a lower quantity at 59.3 °C for 20-min exposure time (1.4 mg/kg). Conclusions: the found model is useful for the prediction of the best temperature/time conditions of the thermal treatment to obtain the lowest contaminates levels in the final product.