Artemisia absinthium and Psidium guajava are powerful sources of secondary metabolites, some of them with potential allelopathic activity. Both the species grow together in India with a weed (Parthenium hysterophorus) that is becoming extremely invasive. The aim of the present research was to test the allelopathic effect of A. absinthium and P. guajava aqueous leaf extracts on seed germination, seedling growth (shoot and root length), as well as some biochemical parameters (enzymatic and non-enzymatic antioxidants, photosynthetic pigments, osmolytes, and malondialdehyde by-products) of P. hysterophorus plants. Leaf extracts of both A. absinthium and P. guajava constrained the germination and seedling development (root and shoot length), affected pigment content (chlorophylls, carotenoids), stimulated the activity of antioxidant enzymes, and increased the level of malondialdehyde by-products of P. hysterophorus plants. Non-enzymatic antioxidants (glutathione and ascorbic acid) in P. hysterophorus leaves were, conversely, negatively affected by both leaf extracts tested in the present experiment. Although A. absinthium was more effective than P. guajava in impacting some biochemical parameters of P. hysterophorus leaves (including a higher EC50 for seed germination), P. guajava extract showed a higher EC50 in terms of root inhibition of P. hysterophorus seedlings. The present study provides the evidence that A. absinthium and P. guajava extract could be proficiently exploited as a botanical herbicide against P. hysterophorus.