The rising shortage of fertilizer resources in crop-producing regions worldwide and the need for fertilizer use optimization to minimize the impact of salt injuries and ammonia toxicity are at the centre of a brewing storm call for sustainable fertilizer savings. The allocation of fertilizers will be an ever-increasing pressure source because of vast agricultural demands under changing climatic conditions. Therefore, starter fertilizers must complement their efficiency and aim to boost productivity and improve food quality to reduce its toxicities, and these observations are corroborated by an analysis of past and ongoing short-, medium-, and long-term experiments. Concurrently, to counterbalance nutrient uptake, fertilizing products containing select nutrients are commonly placed through soil–seed or soil–fertilizer–seed systems to enhance crop production and productivity. Knowledge of the importance of starter fertilizers and their implications as influenced by frequent environmental conditions and management practices remains essential for sustainable and socio-economics of human livelihoods and successful global agronomic food systems under climate change. Therefore, this review takes a closer look at the detailed starter fertilizers’ (N, P, and K) placement approaches exploring their implications on crop production cycles and integrating them with environmental and agronomic management practices that could help to tailor the appropriate fertilizer recommendations and minimise fertilizer toxicity. We explored the mechanisms by which fertilizer salt injury and ammonia toxicity interfere with the morpho-physiological and biochemical processes in most agronomic seed crops. Beyond this, we show the advances that have already been made, as well as suggestions and recommendations concerning managing fertilizer salt injuries and ammonia toxicity potentials in the agricultural industry.