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Branched broomrape an obligate root parasitic weed, has recently re-emerged in California tomato fields in several counties. California is the biggest tomato producer in the US, and the outbreak of this noxious weed could potentially wreak havoc on the industry’s economy. Preventive measures must be taken to stop or reduce the spread of branched broomrape seeds to other areas. Branched broomrape can produce thousands of tiny seeds, which can easily spread with farm machinery over short and long distances. To prevent branched broomrape seed dispersal, sanitation and disinfection of farm equipment are necessary before entering a new farm. We, therefore, tested the effectiveness of various ammonium compounds, including didecyl dimethyl ammonium chloride (DDAC), alkyl dimethyl benzyl ammonium chloride (ADBC), didecyl dimethyl ammonium bromide (DDAB), ammonium bromide (AB), and ammonium chloride (AC) on prevention of branched broomrape seed germination. Dose-response analysis showed that three chemical products, ADBC, DDAB, and DDAC, could completely inhibit (potentially make them non-viable) branched broomrape seeds at 1%, 1%, and 10% w/v concentrations, respectively. These three compounds were further tested in an exposure duration experiment which additionally included Egyptian broomrape. Only 10 minutes of exposure to these compounds was needed to prevent germination of both branched and Egyptian broomrape seeds at 1% (ADBC, DDAB) and 10% w/v (DDAC). Lower concentrations can provide similar inhibition effects when combined with longer exposure times. Egyptian broomrape seeds were more sensitive than branched broomrape seeds. Findings suggest that quaternary ammonium compounds could be used as potential sanitation agents to disinfect agriculture machinery from branched and Egyptian broomrape seeds.