<p>Microplastic (MP) pollution is an emerging threat for the environment as its deteriorating soil biodiversity and agroecosystem. Mainly organic amendments like compost or farmyard waste are considered as the prominent source of MP in agricultural lands. So far, limited studies have investigated the potential of such organic amendments in MP and heavy metals accumulation in soil layers specifically under wheat–maize cropping system. A two-year field trial was conducted to evaluate MP accumulation in poultry litter compost (PLC), municipal solid compost (MSC), farmyard manure compost (FYMC), sludge compost (SC), and vegetable waste compost (VWC) under wheat–maize cropping system. Distribution of MP in soil layers was also investigated. Results revealed that MP contents were 12,782, 14,219, 13,937, 9,759, and 8,714 items kg^-1 in PLC, MSC, SC, FYMC, and VWC, respectively. After two years of organic amendments, MP contamination in soil increased significantly (<i>p</i> &lt; 0.05), reaching 3,483, 3,993, 4,126, 3,476, and 3,561 items kg^-1, respectively. MP abundance was statistically significantly higher in soils amended with organic fertilizers compared to control. The proportion of large MPs (&gt; 1.0&#xa0;mm) in organic materials (57.9%) was higher than in amended soils (49.8%), with reduced MP size and abundance observed in subsurface soils. The shape and polymer composition of MPs were similar in organic materials and amended soils, predominantly comprising fragments of polypropylene, polyethylene, and polyethylene terephthalate fibers. Overall, this research study substantially highlights the threat of MPs pollution in agricultural soils through untreated organic amendments and therefore, it is essential to introduce sustainable novel techniques to mitigate MPs pollution in soil.</p>