In his Kaf Hachaim, noted Rabbinic scholar and Kabbalist, Rabbi Yaakov Chaim Sofer OBM, of Baghdad, quotes various sources about this custom and writes (או”ח תרה, ס”ק כב):
“22) Rashi in Gemara Shabbat 81b states, that the custom was to take a flower pot with plants inside and swing it around the head on Erev Rosh Hashana [Source: Magen Avraham].
Rashi writes in the name of the Geonim (in their responsa), that a few days before Rosh Hashana you should take a flower pot for each of the members of your household, adults and children, and plant in it beans. On Erev Rosh Hashana, once the plant sprouted, each one takes his flower pot, swings it around his head seven times, says “Zeh Chalifasi” and throws it into the river [Source: Machtzis Hashekel].
This seems appropriate for one who cannot do Kapparos on Chickens, and cannot afford money instead of a chicken, that he should do as stated above, with the flower pot.
I saw this solution written in Sidur Yaavetz, where he gives a reasoning, that since the Torah says “Man is a tree of the field” (Devarim 20:19), he shares a connection with the souls of growing plants.
The Pri Chadash states that this custom should be abolished, for he holds like the Beis Yosef, that the custom of Kapparos in its entirety should be abolished (even with regards to chickens). However, for those who hold that it is permitted to perform Kapparos with a chicken, the same would apply to using a flower pot.
But we never hear of any one doing Kapparos on a flower pot, rather everyone does with chickens, and the reason seems to be, because the Arizal stated that Kapparos be performed with chickens, and everyone follows suit.”