We conducted field surveys to detect the population density of the most important invasive weed species and their associated virus vectoring aphids in crops grown under high input field (HIF) vs low-input field (LIF) conditions, with and without fertilizers and pesticides. The most frequent invasive weed species were Stenactisannua, Erigeroncanadensis and Solidagocanadensis. These species were hosts predominantly for the aphids Brachycaudushelichrysi and Aulacorthumsolani in both management systems. The 13% higher coverage of S.annua under LIF conditions resulted in a 30% higher B.helichrysi abundance and ~85% higher A.solani abundance compared with HIF conditions. Host plant quality was assessed by measuring peroxidase enzyme activity. There was a significantly increased POD activity at 10 μmol min −1 mg protein −1 unit in S.annua under LIF conditions, suggesting a higher stress by aphids under this management regime. The high colonization intensity of B.helichrysi on maize, potato and alfalfa crops were detected from both S.annua and E.canadensis. We conclude that new and faster methods need to be used to prevent colonization of such virus vectoring aphids and their host plants, even under low input regimes.