Shallot (Allium cepa L. Aggregatum group) is an important Allium plant commonly grown in tropical countries, including Indonesia, and it is used as spice for daily cooking, medicine, cosmetics and dietary supplements. Since shallot is predominantly propagated vegetatively by bulbs, it augments pathogen accumulation which influences low seed bulb management as well as productivity. Hence, utilisation of seeds/True Seed Shallot (TSS) emerges an alternative propagation material. However, no information is available on the growth stages of shallot plants from TSS. The phenological growth stages of tropical shallot planted in lowland areas using seeds in accordance with the Biologische Bundesanstalt, Bundessortenamt nd CHemische Industrie (BBCH) scale are first described here. Five introduced TSS cultivars, that is, Tuk Tuk, Lokananta, Sanren, Maserati, Tropix and four landraces TSS cultivars, that is, Bima, Biru Lancor, Pancasona and Trisula, were used as planting materials to develop an extended numerical BBCH scale for the identification of different phenological growth stages of shallot from seed. The study was conducted in lowland areas under tropical conditions of Indonesia. Based on BBCH scale, phenology of tropical shallot from seed in lowland area exhibited five of the 10 principal stages (0–9): germination (stage 0), leaf development (stage 1), formation of lateral shoot/tiller of pseudostem (stage 2), development of bulb (harvestable vegetative part) (stage 4), and senescence (stage 9). The codification of the different growth stages is essential in determination of the correct timing for better crop management, particularly for transplanting, fertilisation, control of weeds, disease and pest, plant growth regulators application and harvest time. As an implication, these BBCH scales could be used in plant breeding activities to shorten the TSS life cycle.