Recently, studies about smoked food tend to identify harmful compounds that potentially appear within the smoking process. The process, conducted in a smokehouse, closely corresponds with the design and method. This paper presents a smokehouse designed by integrating a biomass furnace, a heat exchanger, a cyclone separator, and a smoking chamber. The design target was to obtain a smoking system that produces clean smoked fish. The design and construction phase and the performance tests phase are discussed in this paper. The energy source used was coconut shells, fed into the furnace at predetermined amounts, to achieve the desired temperature. The performance tests were done using skipjack fish, whose weight ranged from 0.7−1.0 kg/head. The results showed that the smoking system was able to complete the smoking process of the fish in 13 h with 20.1% moisture reduction. The temperature of the smoking chamber varied from 70 °C to 108 °C and the internal fish temperature during the cooking phase ranged from 71 °C to 80 °C. The temperature performance was supported by a heat exchanger with an effectiveness of 0.63 and a cyclone separator, which channeled the smoke−heat flow, separated fly ash with particle sizes between 0.2−600 µm and tar. Based on the test results, the indirect smoking system developed and tested in this study is shown to be able to perform the smoking fish process satisfactorily and produce clean smoked fish.