The V-tail design gained a reputation as the "forked-tail doctor killer", due to crashes by overconfident wealthy amateur pilots, fatal accidents, and inflight breakups. "Doctor killer" has sometimes been used to describe the conventional-tailed version, as well. However, a detailed analysis by the Aircraft Owners and Pilots Association of accident records for common single-engine retractable-gear aircraft in the United States between 1982 and 1989 demonstrated that the Bonanza had a slightly lower accident rate than other types in the study. Pilot error was cited in 73% of V-tail crashes and 83% of conventional-tail crashes, with aircraft-related causes accounting for 15% and 11% of crashes respectively.
However, the study noted that the aircraft had an unusually high incidence of gear-up landings and inadvertent landing gear retractions on the ground, which were attributed to a non-standard gear-retraction switch on early models that are easily confused with the switch that operates the flaps. Models starting in 1984 use a more distinctive relocated landing-gear switch, augmented by "squat switches" in the landing gear that prevents its operation while compressed by the aircraft's weight, and a throttle position switch that prevents gear retraction at low engine power settings.
In the late 1980s, repeated V-tail structural failures prompted the United States Department of Transportation and Federal Aviation Administration (FAA) to conduct extensive wind tunnel and flight tests, which proved that the V-tail did not meet type certification standards under certain conditions; the effort culminated with the issuance of an airworthiness directive to strengthen the tail, which significantly reduced the incidence of in-flight breakups. Despite this, Beech has long contended that most V-tail failures involve operations well beyond the aircraft's intended flight envelope. Subsequent analysis of National Transportation Safety Board (NTSB) accident records between 1962 and 2007 revealed an average of three V-tail structural failures per year, while the conventional-tailed Bonanza 33 and 36 suffered only eleven such failures in total during the same 45 years. Most V-tail failures involved flight under visual flight rules into instrument meteorological conditions, the flight into thunderstorms, or airframe icing.
In addition to the structural issues, the Bonanza 35 has a relatively narrow centre of gravity envelope, and the tail design is intolerant of imbalances caused by damage, improper maintenance, or repainting. Such imbalances may induce dangerous aeroelastic flutter. Despite these issues, many Bonanza 35 owners insist that the aircraft is reasonably safe and that its reputation has resulted in reduced purchase costs for budget-conscious buyers.
In 1982, the production of the V-tail Bonanza stopped but the conventional-tail Model 33 continued in production until 1995. Still built today is the Model 36 Bonanza, a longer-bodied, straight-tail variant of the original design, introduced in 1968. No Bonanzas were delivered in 2021, but on April 10, 2022, it was announced that production of the Bonanza G36 had restarted.
In January 2012, the Australian Civil Aviation Safety Authority issued an airworthiness directive grounding all Bonanzas, Twin Bonanzas, and Debonairs equipped with a single pole-style yoke and that have forward elevator control cables that are more than 15 years old until they could be inspected. The AD was issued based on two aircraft found to have frayed cables, one of which suffered a cable failure just prior to takeoff and resulting in concerns about the age of the cables in fleet aircraft of this age. At the time of the grounding, some Bonanzas had reached 64 years in service. Aircraft with frayed cables were grounded until the cables were replaced and those that passed inspection were required to have their cables replaced within 60 days regardless. The AD affected only Australian aircraft and was not adopted by the airworthiness authority responsible for the type certificate, the US Federal Aviation Administration. The FAA instead opted to issue a Special Airworthiness Information Bulletin requesting that the elevator control cables be inspected during the annual inspection.
The QU-22 was a Beech 36/A36 Bonanza modified during the Vietnam War to be an electronic monitoring signal relay aircraft, developed under the project name "Pave Eagle" for the United States Air Force. An AiResearch turbocharged, reduction-geared Continental GTSIO-520-G engine was used to reduce its noise signature, much like the later Army-Lockheed YO-3A. These aircraft were intended to be used as unmanned drones to monitor seismic and acoustic sensors dropped along the Ho Chi Minh Trail in Laos and report troop and supply movements. When the project was put into operation in 1968, however, the aircraft were all flown by pilots of the 554th Reconnaissance Squadron Detachment 1, call sign "Vampire". A separate operation "Compass Flag" monitored the General Directorate of Rear Services along the Ho Chi Minh Trail linking to the 6908th security squadron.
Six YQU-22A prototypes (modifications of the Beech 33 Debonair) were combat-tested in 1968, and two were lost during operations, with a civilian test pilot killed. Twenty-seven QU-22Bs were modified, 13 in 1969 and 14 in 1970, with six losses in combat. Two Air Force pilots were killed in action. All of the losses were due to engine failures or the effects of turbulence. A large cowl bump above the spinner was faired-in for an AC current generator, and a higher-weight set of Baron wings and spars were used to handle the 890 L fuel load.