In recent years, interest has surged in the development of plant extracts into botanical nematicides as ecofriendly plant protection products. Aromatic plants are maybe the most studied category of botanicals used in this direction and the yielding essential oils are obtained on a commodity scale by hydro distillation. Nevertheless, can the bioactivity of aromatic plants always be attributed to the terpenes content? What would it mean for soil microcosms to bear the treatment of an essential oil to cure against Meloidogyne sp.? Are there other extraction procedures to prepare more ecofriendly botanical products starting from an aromatic material? Lemon thyme is studied herein for the first time for its nematicidal potential. We compare the efficacy of lemon thyme powder, macerate, water extract and essential oil to control Meloidogyne incognita (Chitwood) and Meloidogyne javanica (Chitwood), and we additionally study the secondary effects on soil microbes and free-living nematodes, as well as on tomato plant growth. According to our results lemon thyme powder enhances tomato plants’ growth in a dose-response manner and when it is incorporated in soil at 1 g kg−1, it exhibits nematicidal activity at a 95% level on M. incognita. The water extract yielding from the same dose is nematicidal only if it is left unfiltered; otherwise only a paralysis effect is demonstrated but inside the soil the biological cycle of the pest is not arrested. The essential oil is good both in performing paralysis and biological cycle arrest, but it detrimentally lowers abundances of bacterial and fungal feeding nematodes. On the contrary, lemon thyme powder and unfiltered water extract augments the bacterial biomass, while the latter also increases the bacterivorous nematodes. Overall, the bio fertilizing lemon thyme powder and its unfiltered water extract successfully control root knot nematodes and are beneficial to soil microbes and saprophytic nematodes.