The firm replaced KPMG in top spot during the second quarter of last year, and has held despite losing three clients.
According to the latest Adviser Rakings, BDO has 144 AIM clients, while KPMG has 139 and Grant Thornton 120.
However, PwC has the most market cap, with £18.14m in billings between its 96 AIM clients. KPMG has £18.64m and BDO £14.43m.
Meanwhile, KPMG has secured top spot on the FTSE AIM 100 market, after gaining two clients. The Big Four firm has now 25 clients, while PwC has 22 and Deloitte and Grant Thornton 12 each.
KPMG topped the list among financial clients, with a total of 30, and PwC retained the most health care clients, at 16. In the industrial and technology sectors, Grant Thornton topped the bill, with 25 and 28 clients in each sector.
BDO came in first place during the first quarter of the year in several sectors, such as basic materials, with 27 clients, consumer goods, with 10 clients, consumer services, with 15, and oil and gas, with 22.
Adviser Rankings pointed out that PwC still lead the FTSE AIM 50 table with 13 clients, followed by Deloitte and KPMG with 8 clients each.
KPMG lost one FTSE AIM 50 client since the previous quarter, but still managed to rise from fourth to third place in client market cap, with a total of £5m.