AbstractCycle threshold (Ct) increase, quantifying plant‐derived DNA fragmentation, was evaluated for its utility as a time‐temperature integrator. This novel approach to monitoring thermal processing of fresh, plant‐based foods represents a paradigm shift. Instead of using quantitative polymerase chain reaction (qPCR) to detect pathogens, identify adulterants, or authenticate ingredients, this rapid technique was used to quantify the fragmentation of an intrinsic plant mitochondrial DNA (mtDNA) gene over time‐temperature treatments. Universal primers were developed which amplified a mitochondrial gene common to plants (atp1). These consensus primers produced a robust qPCR signal in 10 vegetables, 6 fruits, 3 types of nuts, and a biofuel precursor. Using sweet potato (Ipomoea batatas) puree as a model low‐acid product and simple linear regression, Ct value was highly correlated to time‐temperature treatment (R2 = 0.87); the logarithmic reduction (log CFU/mL) of the spore‐forming Clostridium botulinum surrogate, Geobacillus stearothermophilus (R2 = 0.87); and cumulative F‐value (min) in a canned retort process (R2 = 0.88), all comparisons conducted at 121 °C. D121 and z‐values were determined for G. stearothermophilus ATCC 7953 and were 2.71 min and 11.0 °C, respectively. D121 and z‐values for a 174‐bp universal plant amplicon were 11.3 min and 9.17 °C, respectively, for mtDNA from sweet potato puree. We present these data as proof‐of‐concept for a molecular tool that can be used as a rapid, presumptive method for monitoring thermal processing in low‐acid plant products.