SELECT 
  cscart_ult_product_prices.product_id, 
  MIN(
    IF(
      cscart_ult_product_prices.percentage_discount = 0, 
      cscart_ult_product_prices.price, 
      cscart_ult_product_prices.price - (
        cscart_ult_product_prices.price * cscart_ult_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_ult_product_prices 
WHERE 
  cscart_ult_product_prices.product_id IN (
    69132, 69131, 69252, 69412, 69405, 69404, 
    68938, 68937, 68936, 68934, 68933, 
    68932, 68931, 68930, 68929, 68928, 
    68927, 68926, 68925, 68924, 68923, 
    68922, 68918, 68917, 68915, 68913, 
    68857, 68856, 68855, 68854, 68853, 
    68852, 68851, 68849, 68846, 68842, 
    68841, 68840, 68839, 69286
  ) 
  AND cscart_ult_product_prices.lower_limit = 1 
  AND cscart_ult_product_prices.company_id = 1 
  AND cscart_ult_product_prices.usergroup_id IN (0, 0, 1) 
GROUP BY 
  cscart_ult_product_prices.product_id

Query time 0.00054

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_ult_product_prices range usergroup,product_id,company_id,lower_limit,usergroup_id usergroup 13 1 Using where